We all experience cycles of day and night resulting from planet Earth’s rotation around its axis. These daily changes profoundly influence many aspects of life at every level of organisation; from populations to cellular biochemistry. Like humans, other animals as well as plants, fungi, and some bacteria have evolved a biological clock, or circadian clock, to adapt to and anticipate this rhythmicity. In virtually all living organisms on earth, this circadian clock times cellular processes to the appropriate time of day and influences many aspects of health and disease. In our lab, we study the molecular mechanisms of biological timekeeping as well as some of the functional consequences at the biochemical, cellular, and organismal level. 

Circadian timekeeping in a model cell of minimal complexity

Research into circadian timekeeping, and rhythmic regulation of metabolism in particular, is hampered by multiple layers of complexity: population effects, separate but coupled clocks in different tissues, coupled cellular oscillators within tissues or regions of tissues, and an incredible complexity of genetic networks in the clock of every individual cell. Additionally, genomic redundancy and higher ploidy levels in traditional model organisms are a key hindrance in the genetic dissection of clocks. Although great progress has been made in identifying transcriptional clock components, our understanding of rhythmic metabolism and feedback between metabolic and transcriptional rhythms is lagging.

Picture modified from Henderson et al., 2007.

One possible way around these issues lies in the realisation that circadian rhythsm are ultimately a cellular property: A major research line in our lab is to use experimentally tractable model cells of minimal complexity to rapidly generate fundamental understanding of timekeeping. Using the prototypical eukaryotic cells of Ostreococcus tauri, some of our overall aims are to answer the key questions: How do cells keep time? How does a cell align metabolism to the environmental rhythm? Through comparative biology, where results from our model cells are translated to complex organisms that are experimentally less tractable, our fundamental cellular research is expected to directly impact areas of major human challenges, such human and veterinary health or crop improvement.

Comparative chronobiology

Cellular circadian organisation includes substantial temporal organisation of transcription (up to 30% of the genome) to a 24-hour beat. At the core of these daily transcriptional cycles lies a set of 'clock genes' that regulate their own expression via a complex circuitry of transcriptional and translational feedback loops. Although circadian rhythms exist in every eukaryotic lineage, the identities of the oscillating clock genes bear no similarity between taxonomic kingdoms, leading most to consider clock mechanisms in different taxa as separate research areas. 

However, this widespread assumption needs re-evaluation now that accumulating evidence from our lab and many others indicates that the blueprint of rhythmically regulated metabolism translates between all eukaryotic cells. In 2011, we reported three separate ways of proving that cellular timekeeping is maintained without any gene expression in Ostreococcus (O'Neill et al., Nature 2011). A novel circadian rhythm we identified at that time, e.g. rhythmic levels of overoxidised states of peroxiredoxin proteins, was perplexingly observed to be fully conserved across rhythmic organisms, including animals, plants, fungi, and also prokaryotes (Edgar et al. Nature 2012, and several later papers from independent labs). Coupled with numerous observations (both older and very recent) by colleagues our findings suggested rhythmic gene expression alone is insufficient to account for circadian rhythms at the cellular level, and that additional 'non-transcriptional' timing mechanisms must interact with them.

Recently, a collaboration between our laboratory and those of John O'Neill (Cambridge) and Luis Larrondo (Santiago de Chile) led to the discovery of circadian rhythms in the concentration of intracellular magnesium ions, [Mg²⁺]_i, in representatives of each kingdom of eykaryotes (Feeney et al., Nature 2016). Through its role as essential cofactors for nucleoside triphosphates (NTPs), Mg²⁺ is crucial to cellular metabolism. [Mg²⁺]_i rhythms were found to provide an elegantly effective means for dynamically tuning cellular biochemical rates, determining global energy consumption throughout the daily cycle. Importantly, we also found that [Mg²⁺]_i rhythms feed back to regulate clock-controlled gene expression, establishing Mg²⁺ as an effective state variable of the cellular clock, and moreover one that is evolutionarily conserved.

We continue to use Ostreococcus as a starting point for collaborative, comparative studies working with several laboratories worldwide, but most notably and intensively with the O'Neill lab at the LMB in Cambridge. Other collaborators on these projects include Luis Larrondo and Jean-Michel Fustin. 

Circadian rhythms strengthen the plant immune system

Clock disruption in humans, for example by genetic defects or present in the estimated 14% of the UK workforce currently on shift work, increases the incidence of metabolic syndrome, diabetes, cancer, depression and neurodegenerative disorders. In model organisms, clock mutants have been shown to have more severe disease symptoms and to be generally more susceptible.

In plants however, relatively little is known about how circadian clocks affect health. Plants are, like us, under constant attack from a diverse range of potentially pathogenic organisms. Disease is a relatively rare occurrence because plants posses an intricate immune system. However, losses of crop plants due to disease are large, and chemical prevention of disease is highly inefficient, and economically and environmentally costly. With the world's population increasing, the global demand for food will drastically rise. In addition, demand of plant-based energy production is increasing, as emission of greenhouse gasses resulting from the use of fossil fuels needs to be reduced in order to slow down global warming. Possible involvement of circadian clocks in plant health has not been studied in any detail, and given its importance for sustained wealth of the human species, we employ a combination of plant pathology and circadian biology methods to study what aspects of plant immunity are circadially regulated.

Collaborators on this project are Vardis Ntoukakis and Steven Spoel.