Circadian rhythms produce a biological measure of the time of day. In plants, circadian regulation forms an essential adaptation to the fluctuating environment. Most of our knowledge of the molecular aspects of circadian regulation in plants is derived from laboratory experiments that are performed under controlled conditions. However, it is emerging that the circadian clock has complex roles in the coordination of the transcriptome under natural conditions, in both naturally occurring populations of plants and in crop species. In this review, we consider recent insights into circadian regulation under natural conditions. We examine how circadian regulation is integrated with the acute responses of plants to the daily and seasonally fluctuating environment that also presents environmental stresses, in order to coordinate the transcriptome and dynamically adapt plants to their continuously changing environment.

Circadian rhythms are 24‐h biological cycles that align metabolism, physiology, and development with daily environmental fluctuations. Photosynthetic processes are governed by the circadian clock in both flowering plants and some cyanobacteria, but it is unclear how extensively this is conserved throughout the green lineage. We investigated the contribution of circadian regulation to aspects of photosynthesis in Marchantia polymorpha, a liverwort that diverged from flowering plants early in the evolution of land plants. First, we identified in M. polymorpha the circadian regulation of photosynthetic biochemistry, measured using two approaches (delayed fluorescence, pulse amplitude modulation fluorescence). Second, we identified that light‐dark cycles synchronize the phase of 24 h cycles of photosynthesis in M. polymorpha, whereas the phases of different thalli desynchronize under free‐running conditions. This might also be due to the masking of the underlying circadian rhythms of photosynthesis by light‐dark cycles. Finally, we used a pharmacological approach to identify that chloroplast translation might be necessary for clock control of light‐harvesting in M. polymorpha. We infer that the circadian regulation of photosynthesis is well‐conserved amongst terrestrial plants.

Circadian rhythms are 24-hour biological cycles that align metabolism, physiology and development with daily environmental fluctuations. Photosynthetic processes are governed by the circadian clock in both flowering plants and cyanobacteria, but it is unclear how extensively this is conserved throughout the green lineage. We investigated the contribution of circadian regulation to photochemistry in Marchantia polymorpha, a liverwort that diverged from flowering plants early in the evolution of land plants. First, we identified in M. polymorpha the circadian regulation of several measures of photosynthetic biochemistry (delayed fluorescence, the rate of photosynthetic electron transport, and non-photochemical quenching of chlorophyll fluorescence). Second, we identified that light-dark cycles increase the robustness of the 24 h cycles of photosynthesis in M. polymorpha, which might be due to the masking of underlying circadian rhythms of photosynthesis by light-dark cycles. Finally, we used a pharmacological approach to identify that chloroplast translation might be necessary for clock control of light harvesting in M. polymorpha. We infer that the circadian regulation of photosynthesis might be well-conserved amongst terrestrial plants.

Photosynthesis within chloroplasts is crucial for ecosystem function and all agricultural productivity. Chloroplasts are a type of plastid and contain a small circular genome of prokaryotic origin. This genome encodes proteins crucial for chloroplast function and requires correct regulation of gene expression. One cellular mechanism regulating plastid gene transcription involves sigma factors, which in plants are nuclear‐encoded proteins forming part of the chloroplast transcriptional system. These are required for chloroplast gene promoter recognition and transcription initiation, with specific sigma factors thought to recognise specific chloroplast promoters. Plant sigma factors participate in the adjustment of chloroplast transcription in response to environmental fluctuations and during development. They appear to be ancient, originating from photosynthetic bacteria that were chloroplast ancestors, with an increase in sigma factor copy number during plant evolution providing an example of the evolution of cell signalling. We examine the origins, structure, function and environmental signalling by plant sigma factors. Key Concepts Chloroplasts contain a small circular genome that encodes essential components of the photosynthetic apparatus and machinery for plastid transcription/translation. Some higher plant sigma factors participate in the integration of environmental signals that regulate chloroplast gene transcription. Sigma factors are found in bacteria to higher plants. In plants, they are important regulators of chloroplast transcription. Higher plant sigma factors allow the nuclear control of chloroplast transcription, forming a signalling pathway from the nucleus to chloroplasts. Higher plant sigma factors are thought to have evolved from sigma factors of photosynthetic bacteria that were engulfed by eukaryotic cells during the evolution of chloroplasts. During plant evolution, they transferred to the nuclear genome.