LuxR Homolog in a Cottonwood Tree Endophyte Activates Gene Expression in Response to Plant Signal or Specific Peptides

This new gene discovery opens the door for investigating other signals involved in plant-bacteria interactions.

The Science

Scientists discovered a gene in the bacterium Pseudomonas sp. GM79, a beneficial microbe commonly found within the roots of Populus trees (cottonwood), that is activated by signals exuded from the plant.

The Impact

The study’s findings provide a model for investigating a possible new family of signals involved in plant-bacteria interactions that are present in dozens of bacterial species associated with economically important plants.


Many beneficial soil bacteria are associated with plant roots, both outside the root (rhizosphere) and within (endophytic microbes). In Populus, a candidate bioenergy feedstock, the endophyte- and rhizosphere-associated communities are distinct, with a- and ?-Proteobacteria dominating the endophyte communities and Acidobacteria and a-Proteobacteria predominant within the rhizosphere. Proteobacteria isolated from Populus roots have been shown to possess acyl-homoserine lactone (AHL)-type quorum sensing (QS) activity, a cell-to-cell signaling system among bacteria that is dependent on cell density. The AHL QS system includes both signal synthases (encoded by luxI-type genes) and signal receptors (encoded by luxR-type genes), but some of the LuxR proteins have been found to respond instead to plant-derived chemical elicitors. Scientists at Oak Ridge National Laboratory, as part of the Plant-Microbe Interfaces Scientific Focus Area within the Department of Energy’s Office of Biological and Environmental Research, discovered a gene in a Proteobacteria Pseudomonas spGM79 isolated from Populus roots that is a plant signal-activated “orphan” member of the LuxR family of regulatory genes. The gene, pipR, is often flanked by predicted peptidase and peptide transporter genes and is closely related to a gene present in plant pathogens that similarly responds directly to plant-derived signals. Studies support the hypothesis that active transport of a peptide-like signal is required for the signal to interact with PipR, which then activates peptidase gene expression. The identification of a peptide ligand for PipR provides a foundation to identify plant-derived signals for orphan LuxR family proteins.

Principal Investigator

Caroline Harwood
University of Washington–Seattle
[email protected]

BER Program Manager

Kari Perez

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


This work was funded by the Genomic Science program, Office of Biological and Environmental Research, Office of Science, U.S. Department of Energy, as part of the Plant-Microbe Interfaces Scientific Focus Area (


Schaefer, A. L., Y. Oda, B. G. Coutinho, D. Pelletier, J. Weiburg, V. Venturi, E. P. Greenberg, and C. S. Harwood. 2016. “A LuxR Homolog in a Cottonwood Tree Endophyte that Activates Gene Expression in Response to a Plant Signal or Specific Peptides,” mBio 7(4), e01101-16. DOI:10.1128/mBio.01101-16.