How does a plant know where to grow a new root?

That question has now been answered in groundbreaking detail by researchers from Aarhus University and their international collaborators. In a new study, the team reveals how the transport protein LAX3 precisely recognizes and moves the crucial plant hormone auxin - all the way down to the atomic level.

The discovery provides new insight into how plant root systems develop, with potential long-term implications for crop breeding and herbicide mode of action.

“We want to understand how plants communicate internally. This protein is like a mail carrier delivering a very important message at just the right place and time – in this case, auxin to the root where new lateral roots are about to form,” says Bjørn Lildal Amsinck, PhD student at the Department of Molecular Biology and Genetics and one of the study’s lead authors.

One job for one protein: Move the auxin

Auxin is a plant hormone that regulates everything from shoot elongation to root formation. It is often produced in one part of the plant - for instance, the leaves - but needs to be transported elsewhere to have an effect. This is where the AUX/LAX family of transport proteins plays a key role. One of them, LAX3, is especially important for root development.

But how does the protein recognize auxin specifically - and not something else? And how does the molecule physically move through the cell membrane?

To answer that, the researchers combined three cutting-edge technologies:

• Cryo-electron microscopy revealed the three-dimensional structure of LAX3 in three distinct states - both with and without different auxin-like molecules bound.
• Transport assays in frog oocytes measured how efficiently LAX3 moves auxin and related herbicides across membranes.
• Molecular simulations showed how auxin travels to and is released from the binding site, depending on the protein’s charge state.

Together, these approaches provide a uniquely detailed picture of the transport mechanism - and how auxin-like compounds may compete with or block it.

Herbicides: So that’s how they work?

One of the study’s most surprising findings is just how many herbicides - chemicals used to kill weeds - exploit the same “entry route” into the plant as auxin.

“Many of the compounds used in agriculture resemble plant hormones so closely that they hijack the same transport pathways. And it’s kind of wild that we often don’t know how they actually work or move around inside the plant - we just test whether they kill it,” says Amsinck.

The study shows that LAX3 not only recognizes but also transports several of the most commonly used synthetic auxin-like herbicides. Some results even suggest that specific herbicides - which are less chemically similar to auxin - may instead block the transporter itself, preventing it from functioning.

This opens a new chapter in plant chemical biology:

“If we understand how existing compounds work, we can make better-informed choices - and maybe even design herbicides that are more targeted, less harmful, and more sustainable,” he adds.

A piece of the climate puzzle

Although the research is basic science, it also points toward a major applied goal: making plants more resilient to climate extremes.

Root systems are critical to a plant’s ability to take up water and nutrients - and to survive both drought and flooding. Auxin is the signal that initiates root formation. And LAX3 is part of the trigger.

“If we understand how auxin transport works, we might eventually be able to tweak it - and create plants with stronger or more flexible root systems. That could, for example, make them more drought-tolerant,” Amsinck explains.

He emphasizes that this is a long-term, visionary goal - but one that starts with molecular insight:

“We want to move away from trial-and-error and instead make rational decisions in plant breeding. That requires understanding how the system works all the way down to the atomic level.”

International collaboration and new technology

The study is the result of collaboration between Aarhus University, researchers in Munich and New York, and contributions from chemists and bioinformaticians. The project has spanned several years - partly because LAX3 turned out to be an unusually challenging protein to work with.

But with technologies such as cryo-EM and advanced molecular simulations, the team has now succeeded in uncovering the microscopic mechanics of transport.

“The protein is incredibly small - and we’re literally firing electrons at it to see it. It’s not just advanced, it’s essential if we want to understand how plants work at the deepest level,” says Amsinck.

Link to publication: https://www.nature.com/articles/s41477-025-02056-z