Deciphering the Symbiotic Calcium Code: The activation of CCaMK

Lead Research Organisation: John Innes Centre
Department Name: Computational and Systems Biology

Abstract

Plants must acquire their nutrition from their environment and this has led to the increased use of fertilizers. This approach is not a sustainable route for agriculture and alternative methods need to be developed to meet future crop demands. A large number of plants, however, have already developed strategies for obtaining their nutrition via symbioses with bacteria and fungi. Symbioses of legumes with nitrogen fixing bacteria provide the plant with nitrogen in the form of ammonia. Symbioses with fungi provide the plant with phosphorous, other elements, and water.
A holy grail of plant research would be to exploit our understanding of how plants coordinate and promote these beneficial interactions to produce crops that are less reliant on fertilizers. A key part of this process is the generation and decoding of signals that tell the plant what to do. These messages are hidden in calcium oscillations. The aim of this project is to understand how these calcium oscillations lead to the activation of proteins that determine how the plant should develop. Previous studies suggest that an enzyme, protein kinase, may decode these calcium oscillations, thus raising the question how can the same messenger robustly determine different responses? A key question is therefore how calcium oscillations can activate this plant-specific protein kinase. In this proposal we will determine the mechanisms by which the kinase of a model legume (Medicago truncatula) decodes the oscillatory calcium responses. We will achieve this through a multidisciplinary approach using a combination of high resolution imaging of calcium within a root hair with mathematical modelling and detailed biochemical studies of the relevant components.

Technical Summary

Calcium oscillations are known to play a key role in nodulation. However, it is not known how calcium changes activate downstream events that give rise to this important developmental programme. Mycorrhization shares many components of the nodulation pathway, in fact, the nodulation pathway likely evolved from the former. The activation of a calcium and calmodulin dependent protein kinase, CCaMK, is necessary for both processes and genetic studies suggest that the pathways diverge at this point. Within the proposed research programme, we wish to exploit recent advances in location specific cameleon lines that we have engineered into M. truncatula, developments in high resolution confocal imaging, and stochastic spatio-temporal modelling to build 3D models of signal generation on realistic geometries in order to determine the calcium concentration profiles that CCaMK is exposed to. We will reconstruct the spatiotemporal patterns observed in and around the nucleus solving a number of plausible models (CICR, voltage-gated, ligand-gated channels) on realistic geometries using the fire-diffuse-fire framework. These models will be parameterised by values derived from a statistical analysis of confocal images of fine slices of the nuclear membrane. Proteomic approaches will be employed to determine the concentrations of CCaMK and calmodulin (Cam). We will use label-free quantification as our primary method of measuring the abundance of CCaMK and CaM in root hairs. This information will be combined with detailed studies on the phosphorylation dynamics of key residues within CCaMK as a function of calcium concentration and the kinetics of calcium and calmodulin binding to unravel the mode of activation of CCaMK and the decoding strategy.

Planned Impact

Increasing populations, limited energy resources, and global climate change are placing unprecedented challenges on food production. Improved plant nutrition has led to crop yield increases and the continued use of inorganic fertilisers is essential to maintain existing production levels. It is often the essential nutrients nitrogen and phosphorus that limit plant growth, and several plant species have established symbiotic relationships with microorganisms to overcome such limitations. In addition to the symbiotic relationship with arbuscular mycorrhizal fungi that many plants enter into to secure their phosphorus (and water and other nutrients) uptake, legumes also establish interactions with rhizobial bacteria that result in fixed atmospheric nitrogen being transferred to the plant.

Understanding how these processes are governed and the intrinsic signalling pathways that give rise to specificity is a first major step towards the exploitation of this knowledge for engineering crops for the future that have reduced requirements on inorganic fertilisers. Although this project is fundamental by nature, it will provide important insights into the mechanisms by which perinuclear symbiotic calcium oscillations are generated, transmitted and decoded. Exploitation of these results will lead to a more targeted approach to manipulating these pathways in future crops.

Another area of impact of the proposed work lies in training. The postholders will work very closely together and receive well rounded interdisciplinary training in mathematical modelling of spatiotemporal problems, confocal imaging, image processing software, biochemical techniques, binding kinetics, and legume biology. These are all highly valuable skills that can be transferred to a wide range of problems.

The results of this research will be communicated to other researchers through the standard channels of publications, seminars, posters and conference presentations. We will also actively engage in explaining our research to the general public and established mechanisms are in place for facilitating this communication process (Teacher Scientist Network, Friends of John Innes events, Science Art Writing school days, etc).

Publications

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Charpentier M (2013) The role of DMI1 in establishing Ca (2+) oscillations in legume symbioses. in Plant signaling & behavior

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Delaux PM (2015) Algal ancestor of land plants was preadapted for symbiosis. in Proceedings of the National Academy of Sciences of the United States of America

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Livina VN (2015) Tipping point analysis of atmospheric oxygen concentration. in Chaos (Woodbury, N.Y.)

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Martins TV (2019) An Information-Theoretical Approach for Calcium Signaling Specificity. in IEEE transactions on nanobioscience

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Martins TV (2013) Towards the Physics of Calcium Signalling in Plants. in Plants (Basel, Switzerland)

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Martins TV (2016) Nuclear pores enable sustained perinuclear calcium oscillations. in BMC systems biology

 
Description Higher organisms use calcium as an internal signal to transmit information. Plants use calcium to encode signals from their environment and calcium signals have been associated with various biotic and abiotic stresses. Calcium oscillations occur during the establishment of symbiotic interactions between plants and microbes and this symbiosis is key for nutrient acquisition. Yet how these signal convey information and how this information is decoded remains unclear. Through a combination of genetics, biochemistry and mathematical modelling, we identified the underlying mechanism for how plants decode calcium oscillations that govern the symbiotic interactions between plants and microbe. Furthermore we have shown have the protein the decodes calcium oscillations is conserved throughout evolution and was a key innovation that enables plants to colonise land. We also investigated how calcium signals are transported between cytosol and nucleus and proposed a mechanistic models which explains the function of diffusion and nuclear pores in the process. Furthermore, as part of an ongoing collaboration, we identified the calcium channel that is responsible for generating symbiotic calcium oscillations. These findings are significant for understanding how plants establish beneficial interactions with microbes.
Exploitation Route Our mathematical models will be of interest to those working in signaling and in particular calcium signaling. We are taking the biological findings forward in a number of ways that will help elucidate the precise calcium decoding mechanism further. Our statistical analyses for calcium time series are finding applications in related areas. Our findings are likely to be built on by a number of other groups working in the area of symbiosis and signaling.
Sectors Agriculture, Food and Drink

 
Description NRP DTP
Amount £95,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2016 
End 09/2019
 
Title FDF 
Description We developed a computational approach which allows for the simulation of calcium oscillation between compartments (such as the nucleus and cytosol) or between cells. 
Type Of Material Computer model/algorithm 
Year Produced 2016 
Provided To Others? Yes  
Impact This approach allowed us to simulate oscillations emanating from the cytosol in the nucleus, thus enabling us to explore mechanisms for propagation. This work suggested that the calcium machinery for generating oscillations also needs to the present in the nucleus. This prediction led to new experiments which confirmed the predictions and identified channels and pumps on the inner nuclear membrane. The same methodology was used in a new collaboration to explore cell to cell communication via calcium waves. 
 
Description Calcium ROS waves 
Organisation University of Wisconsin-Madison
Country United States 
Sector Academic/University 
PI Contribution We developed a mathematical model for calcium waves in Arabidopsis in response to salt stress. This model suggests a tight link between calcium waves and reactive oxygen species. Based on predictions from the model new experiments were carried out that validated our hypotheses.
Collaborator Contribution Our collaborators carried out the initial experiments that determined the existence of calcium waves and measured their propagation speeds. Based on our mathematical model, further experiments were carried out that clearly established a role for reactive oxygen species in transmitting calcium waves over long distances in plants.
Impact We published a paper in Plant Physiology on coupled calcium and reactive oxygen species waves. This work has been described as a 'breakthrough' in following publication. This is multi-disciplinary project involving plant genetics and imaging (Wisconsin) and mathematical modelling (JIC).
Start Year 2015