The ‘off’ button that lets plants make flowers

Research led by School of Arts and Sciences’ biologist Doris Wagner identified a gene that, when stifled, generates blooms.

Scanning electron microscope image of plant parts. Main image is covered in spikes, smaller one looks smoother and less complex.
AA 10-day-old Arabidopsis seedling displayed no defect in forming new organs (main image), unless they lacked the key genes MP, ETT, and ARF4. In that case, a small stubby plant (inset) that cannot form new organs is the result. (Image: Wagner lab)

Plants must be eminently flexible. While most animals are born with all the organs they’ll ever have, plants generate new organs, including flowers, leaves, and branches, throughout their lifespan. 

A variety of genes must activate in order for these organs to develop. But, in studying the process of flower formation, University of Pennsylvania biologist Doris Wagner and her lab have discovered how one pathway is stifled in order for flowers to form. 

“Identity is not just what you are; it’s what you aren’t,” says Wagner. “There are so many alternative fates that any cell or tissue type could have in an organism that aren’t realized, and that they’re not realized is part of that identity.”

It’s been known that in animals certain pathways governing the activity of stem cells must be repressed in order to give rise to organs. These findings, published in the journal Nature Communications, represent the first time that the same phenomenon has been demonstrated in plants.

Wagner’s lab has long focused on flower formation, given its central role in both reproduction and in yield in agricultural plants. Recently, they turned attention to those pathways that are repressed in order for this process to proceed. A group of enzymes known as auxin response factors (ARFs) caught the researchers’ eye. ARFs regulate the transcription of DNA into RNA and respond to auxin, a plant hormone that governs a wide range of aspects of plant development. One of these is MONOPTEROS (MP), known to activate genes that promote flower formation.

Various images of leaves show normal development of a young plant with leaves and other plants that lack both roots and leaves.
In contrast to a normally developing seedling, interfering with the pathways that govern flower formation, involving MP, ETT, and ARF4, led to the development of plants that lacked roots and leaves. Their apical shoot meristem (bottom center image) was also enlarged. (Image: Wagner lab)

Guided by research conducted by other groups, Wagner’s team looked at two other ARFs that had been found to repress developmental pathways in other facets of plant growth, ETT and ARF4. They noticed that these genes were expressed in the primordial “founder” cells of the plant—those that give rise to flowers—leading the researchers to suspect that these ARFs may have a role to play in flower formation. To nail down their involvement, Wagner and colleagues created a mutant plant that lacked normal levels of MP, ETT, and ARF4. They wound up with very odd, triangle-shaped plants that failed to develop any organs whatsoever: no flowers, leaves, or branches.

“We got this very severe phenotype where the plants don’t make any lateral organs from the embryo,” Wagner says. “Even the embryonic leaves don’t form, and you have this very large meristem, the pocket where stem cells are harbored. So clearly stem-cell fate, or pluripotency, needs to be shut off in order for organogenesis to occur.”

The Penn-led team also observed that levels of SHOOT MERISTEMLESS (STM), a gene involved in maintaining a pool of stem cells, which can give rise to a variety of cell types, was highest in the triple mutant.

“What this was saying to us,” says Wagner, “is that, when STM is present in this region, it prevents plants from making an organ.” Indeed, when the researchers artificially enhanced levels of STM in plants, the plants made even more flower-less “pin” stems; in contrast, blocking STM allowed flowers to form.

Having established the involvement of these elements, the researchers wanted to know more about the interaction between them and how STM is shut off. One possibility was that ETT, ARF4, and STM acted in the same direct pathway as MP. While the team found MP did have an effect on the STM pathway off, it was not directly involved in shutting off STM. Through an intermediary gene, FIL, MP indirectly repressed STM. In a parallel pathway, ETT and ARF4 acted directly to repress STM and give rise to flowers.

A headshot of biology professor Doris Wagner
Doris Wagner

Further investigating led to the realization that ARF4, ETT, and FIL’s repression arose due to their ability to recruit enzymes that compress chromatin—tightly packed DNA—to the STM gene, preventing it from being expressed.

Wagner and her team are still uncovering the details of this process. They don’t know now whether levels of these repressive genes (ARF4, ETT, and FIL) must rise to achieve flower formation, or whether it’s their ability to join together in a complex that allows them to carry it off. Another question of interest is precisely how auxin, the powerful plant hormone, is controlling the process from the top down.

Tinkering with STM accumulation to enhance yield in plants of agricultural value is tricky, since that gene is also the guardian of stem cells, Wagner says. Yet STM is also involved in a phenomenon of which there are many examples of in nature: the shape of leaves, which are simpler in form when STM is shut off. This species-specific characteristic is used for plant classification, gives rise to a plethora of different ornamental plant forms, and underscores the centrality of the STM “off button,” a ripe topic for further research.

Wagner’s coauthors were Yuhee Chung, Yang Zhu, Miin-Feng Wu, and Run Jin of Penn; Sara Simonini, Andre Kuhn, and Lars Østergaard of Norwich Research Park; and Alma Armenta-Medina and C. Stewart Gillmor of Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CIVESTAV-IPN).

The study was supported by the National Science Foundation (Grant 1557529), a University of Pennsylvania University Research Foundation Grant, the Biotechnological and Biological Sciences Research Council, CONACyT Ciencia Básica, and CINVESTAV.

Doris Wagner is the Robert I. Williams Term Professor of Biology in the School of Arts and SciencesDepartment of Biology at the University of Pennsylvania.