Salk Institute
Jeffrey A. Long
Associate Professor
Plant Molecular and Cellular Biology Laboratory
Hearst Foundation Developmental Chair
Jeffrey A. Long

Associate Professor
Plant Molecular and Cellular Biology Laboratory
Hearst Foundation Developmental Chair


Plants develop along a polar axis, with an apical shoot system at the top and a basal root system at the bottom. The shoot system is responsible for all of the above ground portions of the plant such as leaves, branches and flowers, and is the site of photosynthesis. The root system lies below the ground and provides water and nutrients to the plant. This shoot/root system develops early during plant embryogenesis and is fully formed in the mature seed.

My lab's research is focused on how this root/shoot system forms. In other words, we are interested in how a plant embryo develops apical/basal polarity. We are taking a genetic approach to answer this question using the plant model organism Arabidopsis thaliana. By isolating mutants that are disrupted in this process and then cloning the genes responsible, we are gaining insight into the molecular mechanisms the plant uses to determine its polarity. One mutant we have isolated, topless, transforms the apical shoot system into a second, basal root system, giving rise to a seedling with roots at both poles. We have cloned the gene responsible for this transformation and find it encodes a protein that prevents the transcription of root specific genes in the shoot system. We are currently cloning other genes that are involved in the same process, and have found that two of them are highly conserved with genes found in animals and humans.

Figure 1. In a wild-type embryo, the root cap specific marker J1092 is expressed only in the root pole (1°). In topless-1 mutants, expression is found at both poles indicating a transformation from shoot to root fate (2°)

"A plant's shoot system is responsible for all of the above-ground portions of the plant, such as leaves, branches, and flowers, and is the site of photosynthesis. The root system lies below the ground and provides water and nutrients to the plant. My lab's research is focused on how a plant embryo sets up this apical/basal polarity."

Controlled by a tightly regulated choreography that determines what goes up and what goes down, plant embryogenesis establishes a very simple structure that contains two stem cell populations: the shoot meristem, which will give rise to all the "above-ground" organs such as the stem, the leaves, and the flowers, and the root meristem, which gives rise to roots. While investigating why a defective TOPLESS gene messes with a plant's basic architecture–mutant embryos develop into a seedling topped with a second root instead of a stem with leaves–Long and his team discovered that functional TOPLESS codes for a repressor protein that inactivates the genes that otherwise would cause root development in the shoot area of the plant. Their latest study revealed that these fate-transforming genes are two familiar characters: PLETHORA 1 and 2, which had been known to act as master regulators that determine the identity of the root meristem. Without TOPLESS to keep them turned off, the two PLETHORAs are free to impose their will on the top half of the plant embryo, causing the development of a second root instead of a shoot.

With the "below-ground" hierarchy worked out, the question of how the identity of the shoot meristem is determined was still unanswered. Trying to unearth the missing master regulators of shoot development, the researchers searched through tens of thousands of mutant plants till they hit on a member of the CLASS III HD-ZIP transcription factors, known as PHABULOSA, that fit the bill. When forcefully expressed in the traditional territory of the PLETHORA duo, PHABULOSA transformed the root into a shoot, resulting in a seedling with leaves on both ends. Further studies revealed an antagonistic relationship between the PLETHORA and HD-ZIP III genes, ensuring that they stay where they belong and don't get in each other's way.

Understanding these mechanisms at a molecular level is one of the key areas of fundamental plant biology, which could be used for developing agricultural plants with more desirable traits.

Lab Photo

Left to right:
Naden Krogan, Peter T. Smith, Rhiannon Biddick, Rebeca Gonzalez Bayon, Jared Sewell, Dior Kelley, Bas van Schooten, Jeff Long

Selected Publications

Smith, Z.R. and Long, J.A. (2010) Control of Arabidopsis apical-basal embryo polarity by two antagonistic transcription factor families. Nature  464(7287), 423-426.

Szemenyei, H., Hannon, M. and Long, J. (2008) TOPLESS mediates auxin dependent transcriptional repression during Arabidopsis embryogenesis. Science  319, 1384-1386.

Long, J., Ohno, C., Smith, Z., and Meyerowitz, E. (2006). TOPLESS regulates apical embryonic fate in Arabidopsis. Science  312, 1520-1530.

Long, J., Woody,S., Poethig, S., Meyerowitz, E. M., Barton, M. K. (2002). Transformation of shoots into roots in Arabidopsis embryos mutant at the TOPLESS locus. Development  129, 2297-2306.

Awards and Honors

  • Ray Thomas Edwards Foundation Career Development Award
  • Helen Hay Whitney Postdoctoral Fellowship


Long lab

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