Final Report Summary - EXPANSION (A combined post-genomic, biochemical and biophysical investigation to model the systems biology of embryo cell expansion and seed germination in Arabidopsis thaliana)
The objective of this proposal was to develop a multi-scale understanding of the plant cell expansion. Using seed germination as a model system and a combination of novel bioinformatica and image analysis, methods were developed and integrated towards this goal. The specific objectives of the work include the prediction and functional characterisation of genes and gene networking regulating plant cell expansion, characterisation of the biomechanical forces that drive cell expansion, characterisation of a biochemical pathway that drives cell expansion and the integration of these diverse data types into a multi-scale model capturing these processes.
We collated and analysed publicly available gene expression data in two different ways in an effort to uncover genetic interactions regulating plant-cell expansion and uncover previously uncharacterised regulators of this process. The first approach used statistics to correlate the expression of genes across samples, and led to the network termed SeedNet, and the identification of 11 previously uncharacterised regulators of seed germination. This work was published in Proceedings of the National Academy of Sciences (NAS) in the United States of America (USA) with the researcher as both the first and corresponding author, while receiving the cover image of the journal. The second approach involved the development of a novel gene association metric using a machine learning algorithm. The approach was termed co-predicition, and involved the generation of 'rules' by the machine learning algorithm that predict developmental outcome in seeds. These rules were very accurate in their ability to identify genes involved in the same developmental pathway, and using these, and additional 4 previously uncharacterised regulators of seed germination were identified. This work was published in The Plant Cell with the researcher as the first and corresponding author.
The biomechanical forces driving plant cell expansion were investigated using novel computational approach involving the digital reconstruction of three-dimensional (3D) cell shapes. This analysis of dynamic 3D changes in cell shape over time is the first of its kind in plants, and is enabling fundamental questions of plant growth to be answered. A sub-domain of expanding cells within the germinating plant embryo have been identified and provide a cellular target upon which to focus study.
Gene network models generated in the first phase of the project are currently being integrated with this high resolution 3D analysis of changes in plant cell shape. Through multichannel confocal microscopy, gene and protein abundance are being simultaneously quantified within the context of changes in 3D cellular geometry. Candidate genes predicted from the network models were accurately placed within the context of cell shape changes occurring during seed germination. Additionally, a homeodomain transcription factor that acts to regulate these targets has been predicted from the networks, representing the identification of a spatially and temporally regulated gene regulatory network that modulates plant cell expansion.
The quantitative data that are being generated using this multidimensional imaging methodology developed during this fellowship are being used to develop a mathematical model describing cell shape change in germinating embryos. This long-term goal is unfortunately falling outside the window of funding provided by this fellowship. A biochemical pathway involved in the modulation of cellular osmoregulation is being investigated as a possible mechanism for driving intracellular increases in water potential driving cell expansion. A candidate gene has been identified representing a key step in this biochemical pathway, and seeds lacking this gene show a greatly increased capacity for cell expansion. Additional experiments are underway to verify the direct action of this pathway in controlling water uptake in expanding plant cells.
Plant growth is a fundamental component of agriculture and world-food production. The expansion of plant cells is a key component to the growth of crops. The expansion of plant cells and the associated modifications to their surrounding cell walls is significant for the production of plant-based bioenergy. The identification of transcriptional networks modulating these events provides an opportunity to modulate these traits in plants leading to increase food and energy production. The use of seed germination in this work enables these findings to be applied to this system. The global seed trade is a EUR 35-billion annual industry, and the ability to enhance the germination associated traits of these agricultural units represents a significant possibility.
We collated and analysed publicly available gene expression data in two different ways in an effort to uncover genetic interactions regulating plant-cell expansion and uncover previously uncharacterised regulators of this process. The first approach used statistics to correlate the expression of genes across samples, and led to the network termed SeedNet, and the identification of 11 previously uncharacterised regulators of seed germination. This work was published in Proceedings of the National Academy of Sciences (NAS) in the United States of America (USA) with the researcher as both the first and corresponding author, while receiving the cover image of the journal. The second approach involved the development of a novel gene association metric using a machine learning algorithm. The approach was termed co-predicition, and involved the generation of 'rules' by the machine learning algorithm that predict developmental outcome in seeds. These rules were very accurate in their ability to identify genes involved in the same developmental pathway, and using these, and additional 4 previously uncharacterised regulators of seed germination were identified. This work was published in The Plant Cell with the researcher as the first and corresponding author.
The biomechanical forces driving plant cell expansion were investigated using novel computational approach involving the digital reconstruction of three-dimensional (3D) cell shapes. This analysis of dynamic 3D changes in cell shape over time is the first of its kind in plants, and is enabling fundamental questions of plant growth to be answered. A sub-domain of expanding cells within the germinating plant embryo have been identified and provide a cellular target upon which to focus study.
Gene network models generated in the first phase of the project are currently being integrated with this high resolution 3D analysis of changes in plant cell shape. Through multichannel confocal microscopy, gene and protein abundance are being simultaneously quantified within the context of changes in 3D cellular geometry. Candidate genes predicted from the network models were accurately placed within the context of cell shape changes occurring during seed germination. Additionally, a homeodomain transcription factor that acts to regulate these targets has been predicted from the networks, representing the identification of a spatially and temporally regulated gene regulatory network that modulates plant cell expansion.
The quantitative data that are being generated using this multidimensional imaging methodology developed during this fellowship are being used to develop a mathematical model describing cell shape change in germinating embryos. This long-term goal is unfortunately falling outside the window of funding provided by this fellowship. A biochemical pathway involved in the modulation of cellular osmoregulation is being investigated as a possible mechanism for driving intracellular increases in water potential driving cell expansion. A candidate gene has been identified representing a key step in this biochemical pathway, and seeds lacking this gene show a greatly increased capacity for cell expansion. Additional experiments are underway to verify the direct action of this pathway in controlling water uptake in expanding plant cells.
Plant growth is a fundamental component of agriculture and world-food production. The expansion of plant cells is a key component to the growth of crops. The expansion of plant cells and the associated modifications to their surrounding cell walls is significant for the production of plant-based bioenergy. The identification of transcriptional networks modulating these events provides an opportunity to modulate these traits in plants leading to increase food and energy production. The use of seed germination in this work enables these findings to be applied to this system. The global seed trade is a EUR 35-billion annual industry, and the ability to enhance the germination associated traits of these agricultural units represents a significant possibility.