Tag Archives: protein

genome sequencing

Quest for missing proteins in rice genome sequencing

The international team of scientists from Australia, Iran and Japan say there’s an estimated 35,000 proteins encoded by the rice genome sequencing, and yet we still don’t have experimental evidence for 82 per cent of them.

This is important because rice is the major food source for more than half the world’s population, and in order for it to grow in warmer climates and with less water we will need to better understand rice at the molecular level, which means carrying out genome sequencing.

“The genome of rice was completed and published in 2001,” says Professor Paul Haynes from Macquarie University, and a co-author of the new study. “So surely we know enough about it now that we should be able to manipulate how it grows to meet our needs? Well, we don’t.”

“What we have for rice, like most of the well-studied plant and animal species, is a good first approximation of what the gene sequence actually encodes for, but there is still a very large amount of information yet to be confirmed.”

Rice is Australia’s ninth largest agricultural export and generates approximately $800 million in revenue each year, but this productivity comes at a significant cost.

Australian farmers use large amounts of water to irrigate their crops. The increasing demand for this water is threatening the sustainability of their rice production.

“It is imperative that we find ways to make rice better adapted to environments with warmer climates and less available water,” says Paul.

One way to do this would be to give commercial rice varieties some of the characteristics of native Australian varieties of rice, he says.

These plants grow vigorously in many wild areas across Australian without additional watering, in part because their roots grow longer and penetrate deeper into the soil allowing the plants better access to underground reserves of both water and nutrients.

“If we could somehow transform commercial rice varieties so that they grow deeper roots, thereby increasing water uptake efficiency while still retaining high grain yields, we could produce more sustainable plants that would help to future-proof the Australian rice industry,” says Paul.

And that’s why finding rice’s remaining missing proteins and completing the genome sequencing is so critical.

Missing proteins are ones that appear to be encoded in the rice’s genes but have not been experimentally confirmed to exist in the rice itself.

The idea of missing proteins originally arose from researchers working on human genome sequencing, says Paul, but it’s equally applicable to important cereal crops like rice.

The Human Proteome Project is making a map of all the proteins encoded by the human genome, to advance the diagnosis and treatment of disease.

Paul’s team took a similar approach when they looked at rice.

Initially they found that 98.5 per cent of the proteins in rice are considered missing. However by mining publicly available datasets and matching this data with information from the rice genome they were able to reduce this percentage of missing proteins to 82 per cent.

“If we are to continue to feed the ever-increasing number of people on our planet, we really need to produce rice which is more sustainable in terms of better water use and better nutrient uptake, while still maintaining current levels of grain production,” says Paul.

“This will require us to understand rice at the molecular level in a way that we have never done previously.

“It is only by understanding in great detail what happens inside a particular cell that we can really understand what goes on at the whole organism level, and how we can potentially change how that particular organism responds to an external set of circumstances or stimuli.”

The team hopes this study will form the basis of a large-scale scale international collaborative project aimed at identifying all the remaining missing proteins in rice.

The study was published in Molecular Plant and co-authored by researchers from Macquarie University, the Agricultural Biotechnology Research Institute of Iran, the University of Tehran, and the University of Tsukuba.

Originally published via Science in Public.

CO₂ cuts nutrition

CO₂ cuts nutrition

Climate change is affecting the Earth, through more frequent and intense weather events, such as heatwaves and rising sea levels, and is predicted to do so for generations to come. Changes brought on by anthropogenic climate change, from activities such as the burning of fossil fuels and deforestation, are impacting natural ecosystems on land and at sea, and across all human settlements.

Increased atmospheric carbon dioxide (CO₂) levels – which have jumped by a third since the Industrial Revolution – will also have an effect on agriculture and the staple plant foods we consume and export, such as wheat.

Stressors on agribusiness, such as prolonged droughts and the spread of new pests and diseases, are exacerbated by climate change and need to be managed to ensure the long-term sustainability of Australia’s food production.

Researchers at the Primary Industries Climate Challenges Centre (PICCC), a collaboration between the University of Melbourne and the Department of Economic Development, Jobs, Transport and Resources in Victoria, are investigating the effects of increased concentrations of CO₂ on grain yield and quality to reveal how a more carbon-enriched atmosphere will affect Australia’s future food security.

CO₂ cuts nutrition
An aerial view of the Australian Grains Free Air CO₂ Enrichment (AGFACE) project, where researchers are investigating the effects of increased concentrations of carbon dioxide on grain yield and quality.

Increasing concentrations of CO₂ in the atmosphere significantly increase water efficiency in plants and stimulate plant growth, a process known as the “fertilisation effect”. This leads to more biomass and a higher crop yield; however, elevated carbon dioxide (eCO₂) could decrease the nutritional content of food.

“Understanding the mechanisms and responses of crops to eCO₂ allows us to focus crop breeding research on the best traits to take advantage of the eCO₂ effect,” says Dr Glenn Fitzgerald, a senior research scientist at the Department of Economic Development, Jobs, Transport and Resources.

According to Fitzgerald, the research being carried out by PICCC, referred to as Australian Grains Free Air CO₂ Enrichment (AGFACE), is also being done in a drier environment than anywhere previously studied.

“The experiments are what we refer to as ‘fully replicated’ – repeated four times and statistically verified for accuracy and precision,” says Fitzgerald. “This allows us to compare our current growing conditions of 400 parts per million (ppm) CO₂ with eCO₂ conditions of 550 ppm – the atmospheric CO₂ concentration level anticipated for 2050.”

The experiments involve injecting CO₂ into the atmosphere around plants via a series of horizontal rings that are raised as the crops grow, and the process is computer-controlled to maintain a CO₂ concentration level of 550 ppm.

CO₂ cuts nutrition
Horizontal rings injecting carbon dioxide into the atmosphere as part of the AGFACE project. Credit: AGFACE

“We’re observing around a 25–30% increase in yields under eCO₂ conditions for wheat, field peas, canola and lentils in Australia,” says Fitzgerald.


Pests and disease

While higher CO₂ levels boost crop yields, there is also a link between eCO₂ and an increase in viruses that affect crop growth.

Scientists at the Department of Economic Development, Jobs, Transport and Resources have been researching the impact of elevated CO₂ levels on plant vector-borne diseases, and they have observed an increase of 30% in the severity of the Barley Yellow Dwarf Virus (BYDV).

CO₂ cuts nutrition
Higher CO₂ levels are linked with an increase in the severity of Barley Yellow Dwarf Virus.

Spread by aphids, BYDV is a common plant virus that affects wheat, barley and oats, and causes yield losses of up to 50%.

“It’s a really underexplored area,” says Dr Jo Luck, director of research, education and training at the Plant Biosecurity Cooperative Research Centre. “We know quite a lot about the effects of drought and increasing temperatures on crops, but we don’t know much about how the increase in temperature and eCO₂ will affect pests and diseases.

“There is a tension between higher yields from eCO₂ and the impacts on growth from pests and diseases. It’s important we consider this in research when we’re looking at food security.”


This increased yield is due to more efficient photosynthesis and because eCO₂ improves the plant’s water-use efficiency.

With atmospheric CO₂ levels rising, less water will be required to produce the same amount of grain. Fitzgerald estimates about a 30% increase in water efficiency for crops grown under eCO₂ conditions.

But nutritional content suffers. “In terms of grain quality, we see a decrease in protein concentration in cereal grains,” says Fitzgerald. The reduction is due to a decrease in the level of nitrogen (N2) in the grain, which occurs because the plant is less efficient at drawing N2 from the soil.

The same reduction in protein concentration is not observed in legumes, however, because of the action of rhizobia – soil bacteria in the roots of legumes that fix N2 and provide an alternative mechanism for making N2 available.

“We are seeing a 1–14% decrease in grain-protein concentration [for eCO₂ levels] and a decrease in bread quality,” says Fitzgerald.

“This is due to the reduction in protein and because changes in the protein composition affect qualities such as elasticity and loaf volume. There is also a decrease of 5–10% in micronutrients such as iron and zinc.”

This micronutrient deficiency, referred to as “hidden hunger”, is a major health concern, particularly in developing countries, according to the International Food Research Policy Institute’s 2014 Global Hunger Index: The challenge of hidden hunger.

There could also be health implications for Australians. As the protein content of grains diminishes, carbohydrate levels increase, leading to food with higher caloric content and less nutritional value, potentially exacerbating the current obesity epidemic.

The corollary from the work being undertaken by Fitzgerald is that in a future CO₂-enriched world, there will be more food but it will be less nutritious. “We see an increase in crop growth on one hand, but a reduction in crop quality on the other,” says Fitzgerald.

Fitzgerald says more research into nitrogen-uptake mechanisms in plants is required in order to develop crops that, when grown in eCO₂ environments, can capitalise on increased plant growth while maintaining N2, and protein, levels.

For now, though, while an eCO₂ atmosphere may be good for plants, it might not be so good for us.

– Carl Williams

www.piccc.org.au

www.pbcrc.com.au