Mechanisms and functions of photosynthetic entrainment of the Arabidopsis circadian clock

Lead Research Organisation: University of Cambridge
Department Name: Plant Sciences

Abstract

The circadian clock is a 24 h timing device that controls daily rhythms of activity. In plants, the circadian clock regulates photosynthesis, growth and most aspects of metabolism and development to confer a competitive advantage. We have identified a new pathway in which the sugars made by photosynthesis, the defining metabolic pathway of plants, adjust the timing of the plant circadian clock to ensure that the rhythms of the plant are correctly matched to the local day/night cycle. This newly identified process defines a metabolic dawn.

We wish now to understand the machinery by which the metabolic dawn occurs and understand why the circadian clock is adjusted by the sugars made by photosynthesis.

We will perform experimental studies aimed at understanding the consequence for the circadian clock when the plant is prevented from responding to sugars produced by photosynthesis. We will find out if the daily cycle of sugars is sufficient alone to ensure correct timing of the circadian clock by perform experiments in conditions and mutant plants which prevent the normal light signalling pathways from operating. Using similar approaches to manipulate photosynthesis, we will study how well circadian rhythms are matched to the local day and night environment when photosynthesis is inhibited. This will inform about the contribution of photosynthetic entrainment to the functioning of the entire circadian clock.
We will partner with researchers in Japan to create mathematical descriptions of the regulation of the circadian clock by sugars and the reverse process in which the circadian clock regulates the abundance of sugars. The mathematical analyses will determine if the response of the circadian clock to sugar is primarily to improve circadian clock performance or optimizes plant carbon usage. The predictions of the mathematical models will provide new avenues for experimental testing that would not be arrived at by intuition alone.
We will perform experimental studies to investigate the machinery by which sugars regulate the circadian clock. We investigate whether the genes already known to be involved in other responses of plants to sugars are also involved in the regulation of the circadian clock. We will determine whether sugars regulate gene expression by causing chemical modifications of DNA-binding proteins. We will perform experiments to determine if the calcium ion and calcium-binding proteins are involved in the regulation of the circadian system by sugars. We will inhibit photosynthesis in specific cell-types to determine if sugar signals diffuse through the plant to regulate the circadian clock in neighbouring cells.
To perform this work we have formed a team of researchers with skills in circadian rhythms, chemical modification of DNA-binding proteins, photosynthesis and mathematics.

Technical Summary

We have identified a new pathway by which endogenous sugars produced by photosynthesis entrain the circadian clock of Arabidopsis. Our new finding provides opportunity for insight in to circadian regulation, sugar signalling and the maximisation of growth and minimisation of starvation. We will use a multidisciplinary approach to investigate why the circadian clock entrains to sugar signals, the advantages this confers and the molecular machinery responsible. Our research plan can be considered in three main parts
1. Determining the contribution of photosynthetic entrainment to circadian behaviour through studies in mutant backgrounds and in environmental regimes that manipulate photosynthetic and light signalling entrainment mechanisms.
2. Obtaining a theoretical understanding of whether photosynthetic entrainment enhances circadian performance, carbon metabolism or both, through mathematical analysis. We will perform analysis and simulation in a model of the inter-regulation of the circadian clock and carbon metabolism. The major predictions of these studies will be tested by experimental analyses of circadian rhythms, starvation and growth.
3. We will investigate the molecular basis of photosynthetic entrainment through studies of signalling and the regulation of the PRR7 promoter. We will identify if the entrainment of the circadian clock involves known sugar signalling pathways, transcriptional regulators and/or calcium signalling. Since we have previously determined that the PRR7 gene is critical for sensing of the sugars by the circadian clock, we will examine if sugar regulates PRR7 transcription through alterations in chromatin state. We will determine if photosynthetic entrainment of the circadian clock is cell autonomous or if sugars diffuse to couple circadian oscillators.
This multidisciplinary study combines the strengths of researchers in the fields of circadian clocks, photosynthesis, mathematical modelling, chromatin and transcription.

Planned Impact

WHO WILL BENEFIT?
(1) Academic scientists interested in circadian rhythms and the growth and carbon metabolism of plants
(2) Industrial scientists interested in growth and carbon storage.
(3) Research staff.
(4) The general public.

HOW WILL THEY BENEFIT?
(1) Academic scientists will benefit because we aim to make conceptual advances in understanding the regulation of circadian clocks. Other theoretical and experimental research has the potential to unlock new directions in circadian biology and also in the study of the regulation of growth. We place emphasis in this research programme in gaining insight in to why the circadian system is regulated by sugars and the benefits this confers to the organism. We will ensure maximum impact by publishing our research in a timely manner. The applicants have a track record of publishing in high impact journals and widespread dissemination.

(2) Industrial scientists will benefit because our work focuses on two of the major regulators of yield, the circadian clock and growth. Our focus on conceptual understanding of the relationship between carbon metabolism, growth and the circadian clock underpins applied research in the Agribusiness. We are transferring knowledge from our fundamental studies to our industrial partners e.g. Bayer CropScience (Webb) and Syngenta (Henderson). Monsanto reported that modest alterations in the dynamical behaviour of the circadian oscillator results in a 5% increase in soya bean yield under field conditions.

(3) The PDRA will gain considerable benefit from being employed on the project. This will include training in circadian entrainment and sugar signalling. The practical training in molecular biology of gene regulation and physiology will place the PDRA in a good position for a further career in academia or the industry. The interface with theoretical biologists in Japan will provide the PDRA with broad scientific and cultural horizons. PDRAs from the Webb laboratory have had excellent career advancement. All BBSRC-funded PDRAs in the Webb laboratory have obtained publications in Science or Nature and eight former members of the Webb laboratory have obtained Faculty positions.

(4) The general public will benefit from outreach activities at the Department of Plant Sciences, Cambridge. During Science Week numerous interactive and more formal displays on aspects of plant biology and research are presented and 2,000 - 5000 visit the Plant Sciences displays on 'Science Saturday' which will include dissemination of findings from this project. Webb has developed a website describing the function of the circadian clock and a road show that demonstrates how biological oscillators regulate complex behaviours in plants. This interactive display includes movies, interactive web pages and practical demonstrations using chocolates and string. We take every opportunity to publicise our findings, Dr Webb has appeared on Radio interviews (e.g. BBC Farming Today) and his recent findings have been summarised in media outlets as diverse as the Financial Times and Comedy Central's Colbert Report. It is hoped in the long term that the public will benefit from food security generated from the novel agricultural products that arise either directly or indirectly from our findings. Whilst recognising that in any field of study the translation rate from laboratory finding to industrial product is always low, we make every effort with our industrial partners (Bayer Cropscience) to translate our findings for public benefit.

Publications

10 25 50
 
Description We have discovered the molecular pathways by which sugars affect the functioning of the circadian clock of Arabidopsis. This provides basic insight in to the mechanisms by which plants measure time. We have also shown that regulation of the circadian clock by sugars is required for the correct regulation of the turnover sugars and starch, which is the major limiter of growth. We have quantified how sugars regulate the circadian clock in different conditions, and this helps understand why the circadian clock is regulated by sugars. This provides a new understanding of how circadian timing systems work and also might help understand how to make crops bigger
Exploitation Route The next step is to study these process in the cereals and other crops to determine if genetic alteration could increase crop biomass.
We have begun this process in cereals with two PhD students funded by iCASE awards.
Sectors Agriculture, Food and Drink

 
Description We have used experimental approaches in this award to develop new techniques for investigation with our industrial partners as a tool for searching for wheat with increased yield. A Brazilian researcher has visited the laboratory for two months. This provided scientific and cultural exchange and also English language training . The findings of this award have also led to a successful collaboration with BASF, Ghent, which currently supports two iCASE studentships
First Year Of Impact 2015
Sector Agriculture, Food and Drink
Impact Types Cultural,Societal

 
Description BBSRC Industrial Case Award Steed
Amount £100,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2015 
End 10/2019
 
Description BBSRC Industrial Case Award Taylor
Amount £100,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 10/2021
 
Description Mechanisms and functions of photosynthetic entrainment of the Arabidopsis circadian clock
Amount £539,040 (GBP)
Funding ID BB/M006212/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2016 
End 12/2018
 
Description Collaboration with CTBE 
Organisation Bioethanol Science and Technology Centre (CTBE)
Country Brazil 
Sector Private 
PI Contribution We have provided an intellectual framework for data obtained by Dr Camilla Caldana CTBE . We are currently writing a joint research application to support these developments
Collaborator Contribution Ms Vivianne da Silva (CTBE) spent a two month placement in the Webb laboratory and trained my laboratory in the extraction and measurement of starch. This has been essential for progression of the research programme. Additionally Dr Caldana has provided software for statistical analysis of the findings.
Impact We have submitted one manuscript for publication
Start Year 2016
 
Description Collaboration with Dr Michel Vincentz 
Organisation State University of Campinas
Country Brazil 
Sector Academic/University 
PI Contribution We have provided unpublished data that has allowed our partners to perform experiments that allow us to extend our analysis of how sugars regulate the circadian clock
Collaborator Contribution Dr Michel Vincentz and his research team directly tested a hypothesis that arose from our data about the binding of a transcription factor to a circadian clock gene. They have performed the experiment and provided us with the data for joint publication.
Impact We have submitted a joint publications for consideration by a major journal
Start Year 2016
 
Description Collaboration with Kyushu University 
Organisation Kyushu University
Country Japan 
Sector Academic/University 
PI Contribution We have performed analysis of starch turnover and growth in wild type and mutant Arabidopsis plants to develop and test mathematical models of the dynamic adjustment of the circadian oscillator by sugars
Collaborator Contribution Prof Akiko Satake and Dr Motohide Seki have produced a mathematical model of the regulation of the circadian oscillator in Arabidopsis by sugars and provided predictions derived from the model about plant regulation of carbon containing compounds and the effect on growth. This provides a direct test of the hypotheses we have developed and are testing in this study, and additionally has furthered our thinking on the project
Impact Web has visited Japan twice to further the collaboration. This has resulted in dissemination of the research through presentations at 5 Japanese Universities and one conference in Japan
Start Year 2016
 
Description Collaboration with University of San Paolo 
Organisation University of Sao Paulo
Country Brazil 
Sector Academic/University 
PI Contribution We have provided data sets for analysis by Dr Carlos Hotta
Collaborator Contribution Dr Carlos Hotta has performed bioinformatic analysis of our data identifying a relationship between stress and circadian clock signalling
Impact We have submitted a manuscript for publication
Start Year 2016
 
Description Fascination of Plants Day 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact The PDRA and PI exhibited at the University of Cambridge Botanic Garden for Fascination of Plants Day. We showed demonstrations, movies and had a dressing up box
Year(s) Of Engagement Activity 2017
 
Description Participation in Science Sunday 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact The laboratory prepared an interactive display that described circadian rhythms for the Science Open Day. This usually attracts around 2000 people to the Plant Sciences display area.
Year(s) Of Engagement Activity 2016
 
Description Science Saturday 2016 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Three PDRA supported by the BBSRC will develop a display for science Saturday concerning circadian biology
Year(s) Of Engagement Activity 2016