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Journal of Bacteriology, August 2006, p. 5417-5427, Vol. 188, No. 15
0021-9193/06/$08.00+0     doi:10.1128/JB.00376-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Diverse Flavonoids Stimulate NodD1 Binding to nod Gene Promoters in Sinorhizobium meliloti

Melicent C. Peck, Robert F. Fisher, and Sharon R. Long^*

Department of Biological Sciences, Stanford University, Stanford, California 94305-5020

Received 16 March 2006/ Accepted 8 May 2006

NodD1 is a member of the NodD family of LysR-type transcriptional regulators that mediates the expression of nodulation (nod) genes in the soil bacterium Sinorhizobium meliloti. Each species of rhizobia establishes a symbiosis with a limited set of leguminous plants. This host specificity results in part from a NodD-dependent upregulation of nod genes in response to a cocktail of flavonoids in the host plant's root exudates. To demonstrate that NodD is a key determinant of host specificity, we expressed nodD genes from different species of rhizobia in a strain of S. meliloti lacking endogenous NodD activity. We observed that nod gene expression was initiated in response to distinct sets of flavonoid inducers depending on the source of NodD. To better understand the effects of flavonoids on NodD, we assayed the DNA binding activity of S. meliloti NodD1 treated with the flavonoid inducer luteolin. In the presence of luteolin, NodD1 exhibited increased binding to nod gene promoters compared to binding in the absence of luteolin. Surprisingly, although they do not stimulate nod gene expression in S. meliloti, the flavonoids naringenin, eriodictyol, and daidzein also stimulated an increase in the DNA binding affinity of NodD1 to nod gene promoters. In vivo competition assays demonstrate that noninducing flavonoids act as competitive inhibitors of luteolin, suggesting that both inducing and noninducing flavonoids are able to directly bind to NodD1 and mediate conformational changes at nod gene promoters but that only luteolin is capable of promoting the downstream changes necessary for nod gene induction.

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* Corresponding author. Mailing address: Department of Biological Sciences, Gilbert Lab, 371 Serra Mall, Stanford University, Stanford, CA 94305. Phone: (650) 723-3232. Fax: (650) 725-8309. E-mail: srl{at}stanford.edu.

Present address: Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305.

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Journal of Bacteriology, August 2006, p. 5417-5427, Vol. 188, No. 15
0021-9193/06/$08.00+0     doi:10.1128/JB.00376-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

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