Science1 publisherNot yet confirmed elsewhere2 min readPublished
Cryo-EM shows a methanogen shuts off nitrogen fixation by binding its enzyme into an inactive supercomplex
University of Arkansas researchers used cryo-EM to show a methanogen stops fixing nitrogen by binding its enzyme into an inactive supercomplex. The structure, in Nature, pinpoints the regulatory contact a bioengineer would have to control.
The Scientist · Science desk
What happened
- The regulatory proteins are PII proteins, and the paper names the assembly the methanogen nitrogenase-PII protein supercomplex, by Rajnandani Kashyap and colleagues.
- The supercomplex is the off switch: it assembles when the cell's energy or nutrients run low and keeps nitrogenase from fixing nitrogen while conditions stay poor.
- Signals that track the cell's energy and nutrient levels pull the complex apart and restore the enzyme's activity, so the switch flips back on when resources return.
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Why it matters
- capability With the binding resolved, the off switch becomes a target an engineer can act on: disrupt the PII contact and nitrogenase need not switch off when the cell's resources run low.
- cost Making ammonia the current way means a fossil-fuel energy bill in high-pressure reactors plus downstream damage from field runoff that feeds algal blooms, the costs a biological, ambient-condition route is meant to displace.
- precedent The authors frame the work as groundwork for future biotechnology and sustainable agriculture, so its immediate payoff is understanding of microbial physiology and the nitrogen cycle.
High-resolution cryo-electron microscopy gave the team an actual structure of the off switch. [4] You can see which proteins clamp onto nitrogenase and roughly where they bind. [4] "This discovery reveals an entirely new strategy for regulating one of the most important biochemical reactions on Earth," said Dan Lessner, professor of biological sciences at the University of Arkansas and the study's corresponding author. [7][8]
"The biggest limitation in the growth of plants is often having access to enough nitrogen, even when they have enough sunlight, water and CO2," Lessner said. [9] Nitrogen gas is almost 80 percent of the air, but most organisms cannot use it directly. [1] Nitrogenase can, converting it into ammonia, the base of common fertilizers [2][15], and Lessner says the enzyme "can do the conversion biologically under standard temperature and pressure." [12]
From there his argument runs to crops, and he keeps the 'potentially' in it. The work was done in a methanogen, a methane-producing microbe, not a plant. [3] "Because our studies are genetically based, we could potentially take the genetic information we've learned and move it into plants, such as corn," he said. [16] That, he added, "would allow plants to potentially fix their own nitrogen from the atmosphere and alleviate the need for fertilizer, which would obviously have huge economic, social and environmental impacts." [17] The structure shows only how one microbe decides when to run the enzyme.
A single structure cannot say whether forcing the switch open would help a cell or hurt it. The off state assembles when energy and nutrients are scarce [5], so a cell engineered to keep nitrogenase running would lose the control that normally shuts it down.
What to watch
- Whether the team can show that disrupting the PII contact keeps nitrogenase active in a living methanogen.
- Any attempt to move the methanogen's nitrogenase and its regulatory genes into a plant such as corn, and whether the enzyme folds and works there.
- Independent structures of nitrogenase regulation in other organisms, which would test whether this off-switch strategy is common.
Clarity's read
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Reality
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- [1]
Nitrogen gas makes up almost 80% of Earth's atmosphere, and most organisms cannot use it directly.
- [2]
Nitrogen fixation converts nitrogen gas into ammonia, a process carried out by the enzyme nitrogenase.
- [3]
A collaborative U.S. research team brought together by a research group at the University of Arkansas studied nitrogenase and its regulation in a methanogen, a methane-producing microbe.
- [4]
Using high-resolution cryo-electron microscopy, the team found that methanogen nitrogenase can bind regulatory proteins to form a large inactive complex the authors call a protein supercomplex.
- [5]
The supercomplex functions as a molecular off switch, preventing nitrogen fixation when energy or nutrients are limited.
- [6]
Signals that reflect the cell's energy and nutrient levels can break apart the complex and restore enzyme activity, allowing nitrogen fixation to resume.
- [7]
Dan Lessner, professor of biological sciences at the University of Arkansas, is corresponding author of the study, which was published in Nature.
- [8]
Lessner said: "This discovery reveals an entirely new strategy for regulating one of the most important biochemical reactions on Earth."
- [9]
Lessner said: "The biggest limitation in the growth of plants is often having access to enough nitrogen, even when they have enough sunlight, water and CO2."
- [10]
Current fertilizer production chemically converts atmospheric nitrogen into ammonia in high-pressure reactors powered by fossil fuels.
- [11]
A significant amount of fertilizer runs off the land into streams and waterways, which can lead to algal blooms from eutrophication, habitat degradation and biodiversity loss.
- [12]
Lessner said nitrogenase "can do the conversion biologically under standard temperature and pressure."
- [13]
The study is "Cryo-EM structure of a methanogen nitrogenase-PII protein supercomplex," by Rajnandani Kashyap and colleagues, published in Nature in 2026 (DOI 10.1038/s41586-026-11116-z); the regulatory proteins are PII proteins.
- [14]
The authors say the finding advances understanding of microbial physiology, the global nitrogen cycle and the evolution of nitrogen fixation, and provides insights that could inform future biotechnology and sustainable agriculture.
- [16]
Lessner said: "Because our studies are genetically based, we could potentially take the genetic information we've learned and move it into plants, such as corn."
- [17]
Lessner said moving the genetics into plants "would allow plants to potentially fix their own nitrogen from the atmosphere and alleviate the need for fertilizer, which would obviously have huge economic, social and environmental impacts."
Sources
1 independent publisher whose own reporting we read for this story.
- phys.orgNitrogen fixation 'off switch' discovery could one day help crops make their own fertilizer
1 article · October 8, 2026
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