From Growing Roots, Clues to How Stem Cells Decide Their Fate


Time-lapse footage of a threadlike Arabidopsis root as it grows. Each fluorescent pink dot marks the nucleus of a cell that’s in the process of dividing to produce new cells, which will go on to form the different tissue layers of a healthy root.

The work touches on a fundamental question in biology, said associate research professor Cara Winter: “How do cells acquire their identities?” In other words, “how do you get all of the various cell types that make up an organism?”

Just as the human body is made up of many different kinds of cells -- in the brain, muscles, bones and elsewhere -- plants, too, contain various cell types specialized for different tasks.

Whether in the roots, branches, flowers or leaves, virtually all tissues of a plant descend from small groups of unspecialized stem cells that produce new cells by dividing.

Each time a stem cell divides, it faces a choice: it can either produce two new stem cells like itself, or it can make one copy of itself plus one cell that will branch off to become something new.

It’s the latter process, known as asymmetric division, that generates the myriad cell types needed to form a complex organism like a plant, or a human being.

An obvious question then is: How do dividing stem cells choose one path over the other?

This was the question driving Winter and co-first author Pablo Szekely, both researchers in the lab of late biologist Philip Benfey of Duke, as they watched days of root growth in Arabidopsis thaliana, a spindly member of the mustard family.

The researchers focused on two key regulators of cell division in Arabidopsis -- proteins called short-root and scarecrow that, together, prompt dividing root cells to make the switch.

By labeling these proteins with glowing fluorescent tags, they were able to track the activity of the proteins and their effects on dividing stem cells in real time. Light-sheet microscopy allowed them to peer inside the roots’ translucent tissues for up to 50 hours without harming them.

Counter to previous predictions, the researchers showed that even low levels of these proteins, present early in the process of one cell becoming two, are enough to trigger a switch to asymmetric division.

“All they have to do is reach a certain threshold,” said Szekely, who joined the Benfey lab as a postdoctoral researcher in 2020.

The findings have implications for humans and other animals too, the researchers said.

That’s because, although plants and animals diverged more than a billion years ago, they inherited much of the same basic molecular tool kit -- including many of the same “housekeeping” genes that are necessary for cells to function.

The same genes that regulate cell division in plants like Arabidopsis perform similar jobs in animals, including humans. Previous research shows that when asymmetric division is disrupted, cells can multiply out of control and form tumors.

“Cells need to have a program during development: first divide like this, then divide like that,” Szekely said. “It has to be tightly regulated in order for everything to work.”

This work was funded by the U.S. National Institutes of Health (NRSA 5F32GM106690-02 and MIRA 1R35GM131725), the Howard Hughes Medical Institute, and the University of Southern California.

CITATION: "SHR and SCR Coordinate Root Patterning and Growth Early in the Cell Cycle," Cara M. Winter, Pablo Szekely, Vladimir Popov, Heather Belcher, Raina Carter, Matthew Jones, Scott E. Fraser, Thai V. Truong, Philip N. Benfey. Nature, Jan. 31, 2024. DOI: 10.1038/s41586-023-06971-z