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Linking time and energy in plant genes

Researchers have collated a wide array of data on plant metabolism and the biological rhythms that govern this process. Using this data, they have built new and updated models of gene expression in plants.
Linking time and energy in plant genes
The plant's internal clock network, the circadian clock, is responsible for controlling many aspects of its growth and metabolism. In particular, orchestration of carbon metabolism over the day-night cycle is essential for plant cells to avoid periods of starvation.

With EU funding, the TIMET (Linking the clock to metabolism) project researchers selected three closely linked biological systems to study: the circadian clock, the starch metabolic pathway and the isoprenoid metabolic pathway. Responsible for the production of up to 30 000 biomolecules, isoprenoids include cholesterol, vitamin K and all steroid hormones. Project research relied on the accumulation and integration of large data sets into a complex model – a so-called systems biology approach.

The research results integrated the products of clock gene expression and linked them to multiple clock output pathways. Both transcriptome and proteome data showed that the daily rhythms of molecular productivity are affected by changing day length and metabolic and clock mutations, as well as climate change.

Starch regulation was calculated hourly and results point to a system-level feedback. Interestingly, starch degradation was found to continue during the day. Previous models distinguished between a daily state and another at night. Work highlighted how energy and carbon utilisation are optimised and global factors that control growth rate were identified.

The team also produced a publication showing linked sugar and circadian control of root growth. Furthermore, they discovered key molecules and metabolites, and built data infrastructure to support further research.

Newly developed models revealed new groups and networks of genes that regulate plant metabolism night and day in an unexpectedly flexible system. An overarching framework model was designed based on this new knowledge and tested using a simulated clock mutant to explain the changes in biomass. A first, the TIMET team have linked altered gene expression dynamics to quantitative changes in one of the highest levels of control in the plant.

The metabolic pathways studied in TIMET are among the most important in determining crop yield, for both food and non-food crops. Future work will no doubt be directed to application of the systems approach to the most economically important crops in the agricultural arena as well as other biological systems.

Related information


Plant metabolism, gene expression, circadian clock, metabolic pathway, crop
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