Flowers unfold with surprising precision, despite unruly genes

This finding has important implications for plant engineering, where scientists design artificial gene switches to control growth or behavior. Understanding how plants manage genetic “noise” could also inform research in other fields, from synthetic biology, where predictability is crucial, to research on cancer, where random gene activity can drive tumor evolution.

The research published May 20 in Nature Communications.

“Ultimately, the research challenges the idea that biological precision requires perfect control,” Adrienne Roeder, professor in the Section of Plant Biology in the School of Integrative Plant Science, in the College of Agriculture and Life Sciences and at the Weill Institute for Cell and Molecular Biology, who is corresponding author in the study. “Instead, it shows that nature doesn’t eliminate randomness — it builds reliable systems and processes that work despite it.”

Co-author Shuyao Kong initiated and conducted the work as a graduate student in Roeder’s lab at the Weill Institute for Cell and Molecular Biology. Kong is now a postdoctoral researcher at HarvardMedical School.

The researchers examined thale cress (Arabidopsis thaliana), a small plant in the mustard family, to look at stochastic gene expression — the process through which genes can randomly turn on or off. The team found that genes responding to auxin — a hormone that directs flower growth — were activated in a surprisingly random way from cell to cell, even when the hormone signal was the same. Despite identical instructions, the cells behaved unpredictably.

The team used glowing reporters — molecules that light up with fluorescence when genes turn on — to track three auxin-responsive genes, including one called DR5. They found that even though DR5 activity was ‘turned on’ by auxin, it varied wildly from one cell to the next — not because of differences in auxin levels, but due to random fluctuations inside the cells themselves.

They saw this dynamic taking place at the plant’s sepals, the sturdy green leaf-like organs at the base of the bud that protect the emerging flower. Even though the cells are individually “noisy” and unpredictable, the plant repeatedly produces four protective sepals in a perfect pattern.

“I really thought by the time we got to these four [sepal forming] regions, there would be a lot less randomness — but there’s not,” Roeder said. “Somehow, despite the noise, you still get these very clear patches where sepal organs initiate.”

Although scientists have known that gene activity can be noisy at the molecular level, this study reveals that even important developmental genes triggered by the plant hormone auxin show randomness in individual cells, offering new insight into how plants manage such variability during organ formation.

The study found that two auxin-responsive genes, AHP6 and DOF5.8, showed less randomness than DR5, suggesting that plants may have built-in mechanisms to dampen noise when needed.

The key, the team said, is a process called “spatial averaging.” While individual cells behave inconsistently, groups of cells work together to smooth out the noise, creating a stable, collective signal that the plant can use to guide development.

“The organism can use this randomness when it wants to and ignore it when it doesn’t,” Roeder said. “That’s super powerful.”

The study raises important questions, she said. “Spatial averaging is one way that plants manage gene expression noise, but how exactly does that buffering happen, and under what conditions does it fail?” Roeder said. “How can we incorporate that when we’re trying to engineer our favorite gene to express in interesting places?”

Contributing authors include Byron Rusnak, graduate student in the School of Integrative Plant Science (CALS), and Mingyuan Zhu, postdoctoral associate at Duke University.

The research was supported by the National Institute of General Medical Sciences at the National Institutes of Health.