Defining the role of PIF3-like bHLH transcription factors in the integration of light and cold signalling in Arabidopsis

Lead Research Organisation: University of York
Department Name: Biology


Plants have evolved an amazing ability to alter how they grow and develop in response to signals from their environment. This is critical for their survival as it allows them to synchronise growth and development with seasonal changes. A good example of this is the process of seed germination, which marks the start of growth following a period of quiescence or dormancy. The dormancy state enables seeds to survive in the soil for months to years until the conditions are favourable for growth. The ability to sense environmental conditions is critical for a seed, because once it starts to grow the fragile seedling is extremely vulnerable to all sorts of environmental challenges. Temperature and light are two key environmental signals that influence seed dormancy breakage. In the model plant, Arabidopsis thaliana, dormancy is removed by a combination of cold temperatures and light. This requirement for cold temperatures as experienced in winter ensures that seeds only germinate in spring when conditions are good for growth. The light requirement means that seeds will only germinate when they are at or near the soil surface. Very little is known about how plants integrate cold and light signals. We recently discovered that a protein called SPT represses germination until seeds are exposed to cold. We have also found that a second related protein called PIL5 represses seed germination until seeds are exposed to light. Both SPT and PIL5 belong to a class of proteins called transcription factors, because they regulate expression of specific genes. SPT and PIL5 repress expression of key genes involved in the synthesis of a plant hormone called gibberellic acid (GA). We know from previous studies that GA promotes germination. GA also promotes a host of other responses where it acts by decreasing the activity of DELLA proteins. Our most recent data reveal that removal of these DELLA proteins increases germination frequency. For the first time we now have evidence that links light and cold signals with changes in germination of the seed. The picture that is beginning to emerge is that the transcription factor proteins SPT and PIL5 regulate levels of the plant hormone GA. This GA in turn regulates the DELLA proteins that control germination. However, this is most certainly not the whole story as we have other evidence that suggests the SPT and PIL5 proteins also exert GA independent effects on germination. Intriguingly, this mechanism of germination control in response to signals from the environment also appears to control other physiological processes such as seedling leaf size. We now need to work out the details of this important mechanism. Our ultimate aim is to fully understand the different parts of this process so that we can build a model that allows us to predict the effect of changing environmental conditions on plant growth particularly in the developmental window of seed germination and seedling establishment . How plants respond to different environmental conditions can affect important agronomic traits which impact on crop yield. Knowledge gained through this work could lead to improvement of these traits in important crop plants.

Technical Summary

We have recently discovered that cold and light control seed germination through the bHLH transcription factor SPATULA (Penfield et al., 2005 Curr Biol 15:1998-2006). SPT acts as a light stable repressor of seed germination and is required in dormant seeds for the repression of GA3 oxidase (GA3ox) gene expression. We have also shown that the related protein PIL5 represses seed germination and GA3ox expression in the dark, and have proposed a model whereby SPT and PIL5 form part of a regulatory network coupling seed germination and GA signalling to light and temperature responses. Our more recent unpublished data suggest that SPT and PIL5 act upstream of the DELLA proteins in the control of seed germination. SPT is also required post-germination in the phytochrome controlled cotyledon expansion response, which notably is also acutely temperature sensitive and is subject to DELLA control. SPT has high homology to the PIF-like bHLH transcription factors that play a key role in phytochrome-mediated light signalling. Over-expression of SPT leads to strong phyB-like phenotypes such as elongated hypocotyls. This begs the question as to whether the GA signalling based mode of action of SPT in seed dormancy control also operates at other stages in plant development. Furthermore, very little is known about the mode of action of the PIF-like bHLH TFs, and it is tempting to speculate that they also operate upstream of the growth restraining DELLA proteins. In this proposal we will build on the existing tools and complimentary skills in seed germination and PIF/phytochrome mediated signalling in the Graham and Halliday labs respectively to define the role of SPT and related bHLH transcription factors in the integration of light and cold signalling in Arabidopsis. This work should lead to further high impact publications and intellectual property that could be used to design strategies for the improvement of crop plant performance under sub-optimal environmental conditions.


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Sidaway-Lee K (2010) SPATULA links daytime temperature and plant growth rate. in Current biology : CB

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Stewart Lilley JL (2013) The effects of DELLAs on growth change with developmental stage and brassinosteroid levels. in The Plant journal : for cell and molecular biology

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Vaistij FE (2013) Differential control of seed primary dormancy in Arabidopsis ecotypes by the transcription factor SPATULA. in Proceedings of the National Academy of Sciences of the United States of America

Description This BBSRC funded project ran from 2006 to 2010. The project led to a number of breakthroughs in our understanding of how germination and plant growth in general is controlled in response to signals from the environment, and a new appreciation of the role of the SPT transcription factor. Before the work started we had thought that the SPT protein acts as a messenger of signals from the environment that influence the all-important DELLA proteins. By the end of the project we knew that SPT acts in parallel with the DELLA proteins to restrain growth. SPT acts as a transcription factor that regulates the expression of other genes by binding to their promoter regions. We found that SPT does not directly bind to genes involved in biosynthesis of the plant hormone gibberelic acid (GA) but instead binds to the regulatory regions of at least two other related transcription factors, one of which has been shown to regulate seed germination and the other to regulate growth in response to shade avoidance.
Perhaps the most exciting aspect of our work was the demonstration that the SPT protein accumulates and inhibits plant growth under cool (4-20 degrees C) daytime temperature conditions. This discovery raises the possibility of using the SPT gene to develop crops that can grow better at lower temperatures. Building on the work from this grant we published work in PNAS in 2013 that made further important advances in our understanding of how SPT regulates five other transcription factors during seed development and in so doing regulates seed dormancy status.
Exploitation Route See section above.
Sectors Agriculture, Food and Drink

Description Knowledge of the mechanism underpinning seed dormancy control is transferable to the seed industry and may directly impact UK and global agriculture. Seed dormancy is one of the most important traits to control in a crop and industry still needs to manage and improve this process using molecular breeding tools that could be derived from knowledge attained in this project.
First Year Of Impact 2012
Sector Agriculture, Food and Drink
Impact Types Economic

Title New Arabidopsis lines generated 
Description RESOURCES GENERATED 5 transgenic lines, 5 mutant Arabidopsis lines, 2 introgressed lines. 
Type Of Material Biological samples 
Provided To Others? No  
Impact These lines were used in our subsequent research. 
Description BBC Radio 4 Material World programme interview 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact The project PI, Professor Ian Graham, was interviewed by Quentin Cooper in the BBC Radio 4 'Material World' programme about the new insights in plant dormancy control described in the then newly published 2013 PNAS paper linked to this project, and wider implications of the research.
Year(s) Of Engagement Activity 2013
Description Press release: To germinate or not to germinate, that is the question 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact The press release was widely circulated across the media in both the UK and overseas.

The project PI, Professor Ian Graham, was interviewed on the BBC Radio 4 Material World programme about this research work as a result of the press release.
Year(s) Of Engagement Activity 2013