Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR
Edited by Eva Kondorosi, Hungarian Academy of Sciences, Biological Research Centre, Szeged, Hungary, and approved March 19, 2014 (received for review February 10, 2014)
Significance
Nitrogen nodules formed by the symbiosis of rhizobial microbes and legume roots are essential for fixation of nitrogen in the environment. As part of the symbiosis that leads to nodule formation, a series of changes in gene expression of the Rhizobium must occur. The protein NolR is a global regulator of rhizobial genes for symbiosis and nodulation. Here, we describe the three-dimensional structure of this transcription factor in unliganded and DNA bound forms. These structures show how NolR recognizes asymmetric DNA binding sites and reveal a previously unknown mechanism for conformational switching that alters the energetics of interaction to accommodate variable DNA sequences. Two models for the role of NolR in the regulation of nodulation and symbiosis genes are also proposed.
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. Two possible models for the role of NolR in the regulation of different nodulation and symbiosis genes are proposed. To our knowledge, 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.
Data Availability
Data deposition: The atomic coordinates and structure factors have been deposited in the Protein Data Bank, www.pdb.org [PDB ID codes 4OMY (SeMet NolR•oligo AT DNA), 4OMZ (unliganded NolR), and 4ON0 (NolR•oligo AA DNA)].
Acknowledgments
Portions of this research were carried out at the Argonne National Laboratory Structural Biology Center of the Advanced Photon Source, a national user facility operated by the University of Chicago for the Department of Energy Office of Biological and Environmental Research (DE-AC02-06CH11357).
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Information & Authors
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Data Availability
Data deposition: The atomic coordinates and structure factors have been deposited in the Protein Data Bank, www.pdb.org [PDB ID codes 4OMY (SeMet NolR•oligo AT DNA), 4OMZ (unliganded NolR), and 4ON0 (NolR•oligo AA DNA)].
Submission history
Published online: April 14, 2014
Published in issue: April 29, 2014
Keywords
Acknowledgments
Portions of this research were carried out at the Argonne National Laboratory Structural Biology Center of the Advanced Photon Source, a national user facility operated by the University of Chicago for the Department of Energy Office of Biological and Environmental Research (DE-AC02-06CH11357).
Notes
*This Direct Submission article had a prearranged editor.
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Competing Interests
The authors declare no conflict of interest.
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Cite this article
Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR, Proc. Natl. Acad. Sci. U.S.A.
111 (17) 6509-6514,
https://doi.org/10.1073/pnas.1402243111
(2014).
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