One switch to control them all – unravelling seasonality in plants

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Published on: June 7, 2018

Written by Marie-Anne Robertson and Andrew J. Millar, of the School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland.

Plants make drastic changes to their biology to survive the changing seasons. Yet we know little about how they do this – despite the important clues it could give us on how plants adapt to harsh environments. It is only by studying a long-known anomaly in patterns of gene expression that we discover one answer has been there all along.

Plants are masters at adapting to the changing world around them. Dramatic shifts from day to night, and from season to season, can bring harsh frosts or long droughts that stretch a plant’s survival abilities to its limits. The secret to success is not simply adapting to a change in conditions, instead plants anticipate predictable changes.

Over the last 30 years, molecular genetics has revealed the intricate working of plant’s circadian clock. This molecular circuitry acts as a 24 hour timekeeper, controlling over a third of their genome. It allows plants to make multiple adjustments from day to night, including the movement of leaves, flower opening and their use of nutrients and energy.

The changing seasons, however, require more dramatic biological shifts to guarantee survival. Yet we are still largely in the dark when it comes to understanding the underlying processes. What we know so far comes from detailed studies of the most obvious and visible changes, such as the flowering of many plants in spring. Flowering time is important for agriculture, because it controls when some crops can be harvested.

Plants have a surprisingly simple way of anticipating when spring is on the way. The genes controlling flowering are only expressed at particular points in the day. When this coincides with the right environmental trigger, such as longer daylight hours, it alters the behaviour of the proteins controlled by that gene, triggering flowering. In engineering, this process is called coincidence detection. It ensures that these plants avoid harsh winter conditions and risk their delicate flowers only in longer days.

Beyond beautiful spring blooms, plants must also make big shifts to many, less visible, parts of their biology, such as metabolism and energy use. The question is could a coincidence detector explain these other adjustments? This wasn’t obvious, because the best-known detector was specialised for flowering.

Plants produce a vast number of proteins with different roles in their biology. Studying changes in their levels should provide us with clues into the specific ways plants adapt. Scientists have known for a long time that although the level of some proteins are stable across the day, curiously the genes that dictate their production are still expressed in a rhythmic way. This was long seen as a biological anomaly but it turns out that we have missed the bigger picture by only studying daily rhythms.

In a new publication from Seaton et al (2018), looked at how levels of proteins change in response to the seasons – recreating seasonal daylight hours for the plant Arabidopsis, a commonly used model for other plant species. We studied the proteins involved in the most important aspects of plant biology, those involved in photosynthesis – the conversion of sunlight into energy – and those involved in the storage and use of that energy.

In all over a third of genes in Arabidopsis show a rhythm in their expression and around 1700 proteins changed their levels according to seasonal daylight hours. By simply adjusting our focus, what was once seen as a biological anomaly was revealed to be a master key, which promises to open the door to understanding seasonal change.

Many of the proteins we identified were involved in photosynthesis and energy use, but interestingly some were involved in the plant’s secondary metabolism. This has a wider range of functions including toxic and repellent chemicals that act as the plants defence system and could help to ward off seasonal pests.

The experiments also revealed that the timing of gene expression is key. Those genes with a daily peak of activity in the evening had most effect during long days whereas those that peak in the morning were more effective during short days. As so many plant genes have rhythmic expression, this type of coincidence detection, termed translational coincidence, affected hundreds of proteins in this study.

This simple, yet remarkably powerful, global ‘switching’ mechanism allows plants to make sweeping changes to their biology. Like high street shops stocking up for the upcoming season – whether it is swimwear or winter coats – plants must also select the right options from their extensive protein catalogue. When daily rhythms in gene expression work together with the newly discovered process of translational coincidence it provides plants with a powerful way of mixing and matching vast numbers of proteins to boost their survival.

Further analysis reveals that these findings may not be unique to plants. Analysing data from cyanobacteria and algae indicates translational coincidence could be applied to all photosynthetic organisms. This is starting to provide us with vital insights into how plants, and perhaps other photosynthetic organisms, cope with change. In the future, these fundamental discoveries may pave the way to fine tuning plants biology to make them better suited to harsh environments or even help to expand their geographical boundaries.

Take a look at a video about this work here:

Seaton DD, Graf A, Baerenfaller K, Stitt M, Millar AJ, Gruissem W (2018) Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism. Mol Syst Biol. doi: 10.15252/msb.20177962 Open Access

This article is licensed under the Creative Commons License: Attribution 4.0 International,

The study is reported in the following paper, which is free online: Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism (2018) Seaton, D. D., Graf, A., Baerenfaller, K., Stitt, M., Millar, A. J. & Gruissem, W. Molecular Systems Biology. 14, 3, p. e7962. Link:

All the published data, analysis scripts and results are also freely available on the FAIRDOMHub,

The study involved researchers from the University of Edinburgh, Scotland; the Max Planck Institute in Golm, Germany and the ETH in Zurich, Switzerland.

The study was funded by the European Union FP7 project TiMet (award 245143).

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