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N is for nitrogen: how can we make our crops sustainable?

Dr Mehmet Tufan Oz speaks to us about how he came to work at Earlham Institute with his research on plant gene regulation and bioengineering advancements which could lead to superior crop genomes.

Being the fifth most abundant element in the universe, nitrogen is one of the primary nutrients for the survival of all living systems. Named after the Greek word nitron, for ‘native soda’, and genes for ‘forming’ - nitrogen makes up the proteins and building blocks of DNA - transferring genetic information to the next generation of organisms.

For plants, Nitrogen is also a major component of the biomolecule chlorophyll which allows them to absorb their energy from sunlight through photosynthesis to grow. Although an essential compound, too much can cause problems for the environment, such as pollution as a result of the overuse of chemical-induced fertilisers.

This is where plant engineering comes into play; at Earlham Institute (EI) Dr Mehmet Tufan Oz is working on how plants can efficiently use nitrogen while producing sustainable crops and reducing environmental impact. Tufan speaks to us about how he came to work at the EI with his research on plant gene regulation and bioengineering advancements which could lead to superior crop genomes.

As part of the Patron Group at Earlham Institute, in my research I am studying gene regulatory networks (GRNs) which coordinate cellular events (ie, cell division and growth) underlying complex plant traits - such as responses to changes in the environment due to climate change and crop disease.

The Patron lab has already shown that gene editing tools can be used to engineer plant traits such as carbohydrate profiles. My research interest in the improvement of sustainable crop production using synthetic biology approaches as well as CRISPR genome editing aligned perfectly with this.

In the years I have been working in plant biotechnology and genetic engineering, I’ve been aware of the work done at EI on many platforms, including high impact journals and conferences. Additionally, EI being located at the Norwich Research Park, which has an excellent reputation in plant sciences, was another motivation.

Plant biotechnology and specifically plant synthetic biology conferences are sometimes more niche, helping participants to engage more and this is where I met Dr Nicola Patron, Synthetic Biology Group Leader at EI.

Dr Tufan Oz is a Postdoctoral Scientist within the Patron Group at Earlham Institute

Dr Mehmet Tufan Oz at Earlham Institute

Complex connections

In my current research we are interested in how a complex gene regulatory network (GRN) coordinates plant growth in response to nitrogen.

Nitrogen (N) is an essential nutrient for plant growth and metabolic processes. Depletion of Nitrogen in the soil is perceived as a stress which stunts plant development and leads to reduction in growth and yield. Applications of Nitrogen-containing fertilisers have been critical to increasing crop yield but can have negative environmental impacts.

GRNs include connections between proteins that control gene expression - known as transcription factors (TFs) - and the DNA sequences in the genes they regulate. The types of interactions and their dynamics can alter the transcription of thousands of downstream genes, shaping the growth and development of the plant.

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Applications of Nitrogen-containing fertilisers have been critical to increasing crop yield but can have negative environmental impacts.

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Unpicking genes

We are unpicking how genes within the regulatory gene network work together to interpret the signals of nitrate availability and coordinate plant growth in response.

To do this, we investigate interactions between transcription factors and DNA and apply genome engineering tools, such as CRISPR, to disrupt specific combinations of coding and regulatory gene sequences.

This will contribute new knowledge on the regulation of plant growth in response to changes in the environment, as well as improve plant genome editing technologies.

By identifying critical points of regulation and control within the network, we will learn how plants coordinate the expression of the many genes required to alter growth and development in response to rapid changes in their environment - providing new options for developing sustainable crops that are resilient to nutrient stress or that use available nutrients more efficiently.

We combine tools from molecular biology, plant tissue culture and bioinformatics in our research.

Tufan with arabidopsis samples in the EI labs

Genome editing and agriculture

Currently genome engineering is still in its infant stage for agricultural research. Although recent advances in plant genome editing are encouraging, most research to date has been performed on model organisms.

Translation of fundamental plant science to agriculturally important crops is challenging. Some crops are hybrids, polyploids or simply propagated vegetatively as clones. Genome engineering technologies can help to overcome some of the bottlenecks in crop improvement.

For example, in a recent study that I completed at the University of Florida, we reported sugarcane genome editing with CRISPR technologies as a proof of concept. Sugarcane is a polyploid crop which has great potential for biomass production for energy and biofuels.

Overcoming challenges

Advances in genome editing still face technical barriers such as delivery of genome editing tools to plant tissues and a low frequency of editing.

Critically, for most crops, plant transformation, selection and regeneration relies on plant tissue culture, which poses a significant bottleneck due to the time, cost and labour required.

However, recent technical advances provide great potential for translating research to agriculture. For example, ‘prime editing’ and ‘modified nucleases’, also known as base editors, have made it easier to change a single letter of the DNA code and methods that employ components from plant viruses have made the delivery into some plant cells much simpler.

Additionally, tools from nanotechnology such as carbon nanotubes, lipid- or polymer-based nanoparticles are also providing exciting new opportunities to improve genome editing in a wide range of crops.

In an upcoming Research Topic in Frontiers in Genome Editing in which I will be Guest Editor, we aim to report remarkable achievements from across the scientific community that have overcome some of the challenges of genome engineering in crops.

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Genome engineering technologies can help to overcome some of the bottlenecks in crop improvement.

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Bringing sustainable crops to market

Genome editing technologies may also require regulatory approval, depending on the type of edit and the country they are grown in. More communication and discussion are needed to improve the understanding and the potential of new technologies by growers, consumers and the general public.

Gene editing technologies can create genetic variations in plants that are indistinguishable from those obtained through nature, conventional breeding or mutagenesis approaches. Therefore, genome edited plants do not fit current definitions of genetically modified organisms (GMOs).

However, in some countries genome-edited organisms are subjected to the same regulations as GMOs. This presents another challenge for widespread use of editing technologies in agriculture, which is why it’s critical for scientists to communicate their research to the public and share their expertise with policymakers.

Public trust can be strengthened by transparency of information and research which in turn will impact the utility of genome editing in agriculture.

Tufan in the labs at EI with a petri dish of Arabidopsis plants grown in tissue culture.

Tufan with arabidopsis samples in the EI labs
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Hopefully, [the next steps in our research] will provide us with the knowledge to develop sustainable crops in the future and have a wider impact on society in providing the tools to feed a growing world population.

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Applying our work

The next steps for our research will be to use the knowledge we have gained together with using synthetic biology approaches in order to engineer plant responses to nitrogen.

Hopefully, this will provide us with the knowledge to develop sustainable crops in the future and have a wider impact on society in providing the tools to feed a growing world population.

Synthetic Biology Group Leader at the Earlham Institute, Dr Nicola Patron, said: “Tufan’s work is uncovering new knowledge of how suites of plant genes work together to ‘finetune’ growth in response to the increasing obstacles they face in their changing environment. We are excited about how we can use this knowledge for new ways of crop improvement”.

Tufan’s research is in collaboration with the Brady Group at the University of California, Davis. Keep an eye out for Tufan guest editing the upcoming issue of Frontiers in Genome Editing - if you would like information on submitting an abstract, see here.

Recoding Regulation

We are currently using genome engineering tools and developing synthetic regulatory elements to engineer complex traits in plants by disrupting and rewiring gene regulatory networks that coordinate the growth of plants in response to changes in their environment.

Our research

Hayley London

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