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Using supercomputers to feed and green the world

 Quinoa cropped

A key to feeding humanity and combating climate change through the 21st century will be the development of ‘supercharged’ crops and trees that perform the miracle of photosynthesis with far greater efficiency.

At the Australian National University’s John Curtin School of Medical Research, Professor Jill Gready and her team are employing Australia’s most powerful supercomputer, Raijin, at NCI to unlock the secrets of what has been termed ‘the most important chemical process on Earth’, photosynthesis, which enables plants to use sunlight to convert CO2 to food and fibre – and so support all other life, including us.

At the heart of the process is an enigmatic enzyme, Rubisco, which pulls CO2 from the air enabling plants to convert its carbon into proteins, sugars, starches, oils, celluloses and other useful substances. However, despite a couple of billion years of evolution, Rubisco is still rather inefficient at what it does, leaving plenty of room for improvement, Professor Gready says.

“Our studies aim to find out why Rubisco is so inefficient, and to use this information to re-engineer it for improved efficiency. Even modest improvements offer major scope to enhance light, water and nutrient utilization by plants and, hence, to create higher-yielding food crops, to green deserts and to restore degraded landscapes. Another application could be improved tree Rubiscos that can lock up more CO2 and fight climate change, or adaptation of suitable plants for sustainable high-yield biofuel production,” she explains.

Over the last 30 years Professor Gready has developed a unique multidisciplinary approach for tackling complex bimolecular challenges which has overcome many seemingly intractable problems. This integrates computational and conceptual biology (computation and simulation, bioinformatics, genomics, phylogenetics, prediction) with experimentation across fields such as biochemistry, biophysics, molecular biology and enzymology. “Computer simulation offers us the possibility to obtain detailed information on the conformation, reactions, interactions and other properties of proteins which is unobtainable by experimental means. The key to our approach is to couple computation and experiment at all stages of the project,” she says.

Her team is using the NCI supercomputer to probe the secrets of Rubisco in the quest to identify or develop variants which perform the same basic catalysis tasks – but which do them faster and waste far less energy on unwanted chemical side-reactions.

“Computational simulation of the mechanism of Rubisco is much more challenging than simulations for other enzymes because of the sheer size and complexity of the protein,” she says. “However, if we can do it for Rubisco, we anticipate it will blaze a trail to re-engineering thousands of other enzymes, with valuable applications across the whole of biology, biotechnology, agriculture, medical science and drug design – so it is an ideal target for proof the concept.”

The work has already achieved significant progress developing several ‘mutant’ Rubisco that take up CO2 more efficiently and are more specific in their action. This advance alone could lead to crops with improved water-use efficiency – vital in times of drought or water scarcity. In parallel work, Prof. Gready is scouring the world’s seed banks for naturally occurring Rubiscos with similar propensities.

“The gains we have seen in the lab with our new Rubiscos so far are already much greater than major agribiotech companies would normally aim for when developing a new crop type,” she comments. “Potentially they will enable us to design efficient biofuel crops that don’t compete with food crops for key resources.”

Patents have already been taken out encompassing the Rubisco work and plans for applications in commercial, national and international agriculture for ultimate delivery to farmers are well advanced.

In another project Prof. Gready’s team is using the NCI supercomputer to study a protein similar to prion protein they recently discovered called Shadoo. “Misfolded forms – prions – have had a bad press because of their association with diseases such as Mad Cow and Creutzfeldt-Jakob – but in reality prion protein is a good guy. They are involved in high order brain functions such as memory,” she explains. It is early days in defining the functions of Shadoo but one aspect being studied using NCI is its ability to bind RNA in a similar manner to that of the protein that causes Fragile X syndrome in children. This work may throw light on the causes of this condition.

Through Prof. Gready’s pioneering work on enzymes, Australia’s NCI supercomputer is playing a potent role in the global endeavour to feed humanity, protect the world from climate change and enhance human health.

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