How does plant energy biology function as a whole?

This discovery activity transverses the other three and will serve to tie the three together, provide cohesion and enforce the standardisation and quality control needed to generate high-quality datasets. It will consist exclusively of data analysis, employing data from our three ‘wet-lab’ research areas together with data from international repositories and our collaborative partnerships. Data will be mined for novel correlations to be followed up for breakthrough discoveries and will also be globally analysed with the final aim of producing accurate predictive models of plant energy metabolism. The recent award of funding to create a Western Australian State Centre of Excellence in Computational Systems Biology in conjunction with the ARC Centre of Excellence in Plant Energy Biology will allow us to apply the latest systems biology approaches to our data. Currently this program is primarily at the strategic planning stage.

Our progress towards achieving the Centre's energy systems vision requires the following:

• Defining the major components of the energy systems in plants
• Defining the key links between these components, creating networks
• Modelling the system in sufficient detail to make useful predictions

What are the major components of the energy systems in plants?

Research Highlight

SUBA, the protein localisation database

The knowledge about where in the cell a protein functions is critical for an understanding of all cellular processes, including energy biology. We have constructed the most complete and up-to-date plant database on this topic anywhere in the world. Collation of subcellular location data from in-house and international sources has developed SUBA (Subcellular Location of Arabidopsis Proteins Database) a highly interactive Web resource allowing complex querying of available information on over 6000 proteins in Arabidopsis. SUBA is publicly available at the Centre’s website, and by monitoring its access Centre researchers can confirm that it is used intensely by the research community. In the latter half of 2006, 2065 web addresses external to the Centre placed 11,590 specific queries.

Heazlewood JL, Verboom RE, Tonti-Filippini J, Small I, Millar AH SUBA: The Arabidopsis Subcellular Database. Nucleic Acids Research (in press).

Defining the key links between these components, creating networks

Having defined the pieces of the systems biology jigsaw puzzle, the task of the Energy Systems area then becomes one of making the relevant linkages between them. Such links include protein-protein, protein-RNA and protein-DNA interactions, co-expression data, metabolite/transcript correlations and other statistical, experimentally determined or predicted connections of any sort. The on-going activity of refining these links will itself become a tool for guiding experimental exploration in organelle biogenesis, metabolomics and signalling. The sheer volume and complexity of data already available demands that we allocate effort in our systems activities to the development and deployment of visualization tools to build and map interaction networks.

Model the system in sufficient detail to make useful predictions

A model is only as good as its ability to predict reliably the behaviour of the real system it seeks to replicate. In its path towards this goal, Energy Systems will build complex stoichiometric models of energy metabolism, or key sub-pathways of it. We intend validating the model(s) by modelling the effects of known perturbations to the system (e.g. reproducing the metabolism of specific knockout mutants), and subsequently using the model(s) to make testable predictions of the effects of as yet uninvestigated perturbations to the system. Finally, we intend to use the model(s) to predict necessary changes to make to the system to achieve desired outcomes in biotechnology or agriculture.

Why Systems Biology?

To reach our ultimate goal of designing optimal plants for specific purposes, we need to fully understand how energy metabolism functions as a single, highly coordinated system. This brings us into the realm of ‘systems biology’, a new academic field that seeks to integrate different levels of information to understand how biological systems function as a unit.

The systems biology approach involves cycles of data acquisition, computational modelling and experimental testing to quantitatively describe cellular processes. Since the ultimate objective is a model of all the interactions in a system, the experimental approaches that most suit systems biology are those that are system-wide and attempt to be as complete as possible. Therefore, high-throughput ‘omics’ technologies such as transcriptomics (the study of the expression of all genes), proteomics (the study of all proteins), and metabolomics (the study of all metabolites) are used to collect quantitative data for the construction and validation of models.

Recent advances in high-throughput technologies, such as mass spectrometry and microarrays, are propelling a systems biology revolution. The field is progressing from a qualitative and descriptive science to a quantitative and predictive science. In turn, systems biologists are gaining a molecular- and engineering-level understanding of biology. This new understanding is allowing scientists to create novel biochemical processes and modify biological organisms to achieve predictable results. Systems biology is in its infancy, but is widely believed to become the main research thrust in biological sciences in the 21st century. The ARC Centre of Excellence in Plant Energy Biology shares this vision.

Systems biology requires combined expertise in biology, mathematics and informatics and as such, few students or researchers are adequately trained in this new field. A major output from our Centre will be personnel with the skills and knowledge to make an impact in this exciting and fast-moving research area.