Genetic switch found in legumes that regulates nutrient uptake

Legumes such as beans, peas and lentils stand out among other crops for their ability to interact with soil bacteria to convert or “fix” nitrogen into a form that is assimilable for most organisms. However, this biological process requires a lot of energy from the plant. Therefore, when soils contain high amounts of assimilable forms of nitrogen (through natural processes or by applying synthetic fertilizers), the plant reduces nitrogen fixation, thus avoiding unnecessary expenditure for the organism.

An international team of scientists, including researchers from the Polytechnic University of Madrid (UPM) in Spain, has for the first time identified a genetic “off switch” that stops the process by which legumes convert atmospheric nitrogen into nutrients.

Eliminating the discovered genetic regulator allowed the team to maintain nitrogen fixation when soil nitrate levels are high. Plants could thus continue to use nitrogen from the air regardless of soil conditions.

Increasing the biological capacity of legumes to fix nitrogen could help increase the growth and yield of agricultural crops while reducing the need for synthetic fertilizers, which contribute to the harmful environmental footprint of agriculture.

This research was conducted as part of the international ENSA (Enabling Nutrient Symbioses in Agriculture) project. The ENSA project is currently funded by Bill & Melinda Gates Agriculture Innovations (Gates Ag One), a nonprofit organization that invests in innovative agricultural research to meet the urgent and underserved needs of smallholder farmers in sub-Saharan Africa and South Asia.

“From an agricultural perspective, continued nitrogen fixation could be a beneficial trait that increases nitrogen availability, both for the legume and for future crops that depend on the nitrogen remaining in the soil after the legumes are grown,” explains Dugald Reid, co-author of the study and researcher at ENSA.

“This helps lay the groundwork for future research that will provide us with new ways to manage our agricultural systems to reduce nitrogen fertilizer use, increase farm incomes and reduce the impact of nitrogen fertilizer use on the environment,” he added.

Leguminous plant of the Lotus japonicus species. (Photo: Helene Eriksen)

The team discovered the regulator known as Fixation Under Nitrate (FUN) after examining 150,000 individual legume plants in which genes had been deleted to identify how the plants control the switch from nitrogen fixation to nitrogen uptake from the soil.

FUN, a type of protein known as a transcription factor whose function is to control the expression levels of other genes, was found to be present in legumes regardless of whether it is active or inactive and regardless of nitrogen levels.

“As part of the study, we designed a genetic screen with thousands of plants grown in greenhouses to identify genes that connect environmental signals to biological responses,” explains Jieshun Lin of Aarhus University in Denmark, ENSA researcher and co-author of the study. “By increasing the levels of nitrate available to our model legume, we were able to identify those with impaired regulation of nitrogen fixation and discover the FUN mutant.”

The team then used a combination of biochemistry, gene expression analysis, and microscopy to discover that FUN organizes itself into long protein filaments when inactive. This led to the secondary discovery that zinc levels play a role in triggering FUN to activate and stop nitrogen fixation.

“We found that changing soil nitrogen alters zinc levels in the plant. Zinc had not previously been linked to regulating nitrogen fixation, but our study found that a change in zinc levels in turn activates FUN, which controls a large number of genes that inhibit nitrogen fixation,” explains Kasper Andersen, co-author of the study and researcher at ENSA. “Therefore, removing FUN creates a condition in which the plant no longer blocks nitrogen fixation,” he concludes.

The study is titled “Zinc mediates control of nitrogen fixation via transcription factor filamentation” and has been published in the academic journal Nature.

The team is now investigating how other common legume crops, such as soybeans and beans, behave when FUN loses its activity. (Source: UPM)