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Title: Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory NolR

item LEE, SOON GOO - Washington University
item Krishnan, Hari
item JEZ, JOSEPH - Washington University

Submitted to: Proceedings of the National Academy of Sciences (PNAS)
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/19/2014
Publication Date: 4/14/2014
Publication URL:
Citation: Lee, S., Krishnan, H.B., Jez, J.M. 2014. Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory NolR. Proceedings of the National Academy of Sciences. 111(17):6509-6514.

Interpretive Summary: Rhizobia are soil-dwelling bacteria that form nodules on the roots of legume plants. The nodules are specialized structures where atmospheric nitrogen is fixed by the bacterium, which in turn, is utilized by legumes for growth and development. This process is termed biological nitrogen fixation and it enables legumes to grow in nitrogen-poor soils. As part of the symbiosis that leads to nodule formation, a series of changes in gene expression of the Rhizobium must occur. NolR is a global regulator of Rhizobial genes for symbiosis and nodulation. In this study we describe the three dimensional structure of NolR. Our structural analyses show how NolR recognizes asymmetric DNA binding sites and reveal a previously unknown mechanism for regulation of nodulation. Information obtained from this structural study will help scientists to better understand the factors that limit the formation of nitrogen-fixing nodules on legumes. Such an understanding should enable scientists to manipulate biological nitrogen fixation so that farmers can increase yields with minimal use of nitrogen fertilizers.

Technical Abstract: The symbiosis between rhizobial microbes and host plants involves the coordinated expression of multiple genes, which leads to nodule formation and nitrogen fixation. As part of the transcriptional machinery for nodulation and symbiosis across a range of Rhizobium, NolR serves as a global regulatory protein. Here we present the x-ray crystal structures of NolR in the unliganded form and complexed with two different 22 base pair (bp) double-stranded operator sequences (oligos AT and AA). Structural and biochemical analysis of NolR reveals protein-DNA interactions with an asymmetric operator site and defines a mechanism for conformational switching of a key residue (Gln56) to accommodate variation in target DNA sequences from diverse rhizobial genes for nodulation and symbiosis. This conformational switching alters the energetic contributions to DNA binding without changes in affinity for the target sequence. A model for the role of NolR in the regulation of different nodulation and symbiosis genes is also proposed. These studies provide the first structural insight on the regulation of genes involved in the agriculturally and ecologically important symbiosis of microbes and plants that leads to nodule formation and nitrogen fixation.