When plant cells communicate, plasmodesmata serve as crucial conduits. These channels cross cell walls, linking one cell to its neighbor. If a plant needs to grow larger or fight off a pathogen, molecular signals pass through plasmodesmata to keep cells working in synch. “Plasmodesmata occur between all cells in all plants,” explains lead author William Nicolas, a plant cell biologist and electron microscopist who recently completed his PhD at the University of Bordeaux in France. “They are central to plant physiology.” And yet, scientists still don’t know how they regulate what passes through.

Now, using a powerful microscopy technique known as electron tomography, Nicolas and his team have for the first time captured the three-dimensional structure of plasmodesmata. Their findings, reported in Nature Plants, force them and others to question the basic mechanics of how plant cells communicate.

A single plasmodesma is like a tube within a tube. The outer tube is made from a plasma membrane of lipids and proteins. The inner tube, known as the desmotubule, is made from the endoplasmic reticulum of the connected cells. Molecules pass through a plasmodesma in the space between these outer and inner tubes, a region scientists call the cytoplasmic sleeve. One commonly held working theory is that plasmodesmata can adjust the spacing between the tubes to permit or restrict the passage of molecules of different sizes, hence modulating communications.

To better understand plasmodesmata and investigate the above working theory, Nicolas wanted to take a closer look at the structure. “All the previous models were based on 2-D pictures of plasmodesmata,” says Nicolas. “Our goal was to get a more precise picture.”

He and his team imaged plasmodesmata in cells of Arabidopsis roots using electron tomography, a technique that allows researchers to reconstruct the three-dimensional structure of an object from a series of two-dimensional images taken at different angles. Some of the three-dimensional images matched expectations of what plasmodesmata should look like—an inner tube and an outer tube connected by thin spoke-like structures with space for molecules to travel through.

But in others, the gap between the tubes was missing—the inner tube instead appeared flush against the plasma membrane. At first, Nicolas put these images aside, assuming experimental error. “But then we thought, this must mean something because we see them all the time,” he says. By systematically exploring cells at different stages of development—from newly divided cells to more mature cells—the team discovered that plasmodesmata change form over time. Mature plasmodesmata have the textbook gap between the tubes, which newer plasmodesmata lack.

Nicolas initially thought that without spacing between tubes, molecules would be blocked. To test this hypothesis, the team tracked green florescent protein (GFP) as it moved through cells connected by newly-formed plasmodesmata. The protein made it through.

“What is surprising is that the internal structure [of a newly-formed plasmodesmata] seems to exclude a cytoplasmic sleeve and that’s always been thought to be where the molecules are moving,” says plant biologist Robert Turgeon of Cornell University, who was not involved with the study. But the researchers’ findings, he says, raise more questions than answers about how cells communicate.

The researchers don’t know how molecules are moving through a space that appears to be closed off. If in fact there is some space, they wonder whether the immature plasmodesmata can modulate communications by restricting molecule movement. The team is now identifying the size limit for molecules passing through each of the two plasmodesmata types.

The findings could also inspire research on how viruses spread through a plant. Viruses hijack plasmodesmata to move from cell to cell. Some studies suggest that some viruses only move through mature plasmodesmata, notes study coauthor Lysiane Brocard, also of the University of Bordeaux. Based on Brocard’s and Nicolas’ findings, researchers could explore whether structural differences in plasmodesmata might help explain that viral activity. Indeed, Nicolas, Brocard, and colleagues are currently using electron tomography to peer into the plasmodesmata of virally infected plant tissue.