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

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 111; no. 17; pp. 6509 - 6514
• Main Authors: Lee, Soon Goo, Krishnan, Hari B., Jez, joseph M.
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 29.04.2014; National Acad Sciences
• Subjects: Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Base Sequence; Binding sites; Biochemistry; Biological Sciences; Calorimetry; Crystal structure; DNA; DNA, Bacterial - metabolism; Gene expression; Gene Expression Regulation, Bacterial; Genes; Glutamine - metabolism; Gram-negative bacteria; Models, Biological; Models, Molecular; Molecular Sequence Data; Monomers; Mutant Proteins - chemistry; Mutant Proteins - metabolism; Nodulation; Operator Regions, Genetic - genetics; Phosphates; Plant Root Nodulation - genetics; Protein Binding; Protein Structure, Secondary; Proteins; Rhizobium; Rhizobium - genetics; RNA-protein interactions; Sinorhizobium meliloti; Structure-Activity Relationship; Symbiosis; Symbiosis - genetics; Thermodynamics; Titrimetry; protein structure; transcription factor
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1402243111

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, NoIR serves as a global regulatory protein. Here, we present the X-ray crystal structures of NoIR 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 NoIR 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 frin duverse rhizobial genes fir 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 NoIR 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.