Glutamine synthetase stabilizes the binding of GlnR to nitrogen fixation gene operators.

Biological nitrogen fixation (BNF) is a high energy demanding process carried out by diazotrophic microorganisms that supply combined nitrogen to the biosphere. The genes related to BNF are strictly regulated, but these mechanisms are poorly understood in gram-positive bacteria. The transcription factor GlnR was proposed to regulate nitrogen fixation-related genes based on Paenibacillus comparative genomics. In order to validate this proposal, we investigated BNF regulatory sequences in Paenibacillus riograndensis SBR5T genome. We identified GlnR-binding sites flanking σA -binding sites upstream from BNF-related genes. GlnR binding to these sites was demonstrated by surface plasmon resonance spectroscopy. GlnR-DNA affinity is greatly enhanced when GlnR is in complex with feedback-inhibited (glutamine-occupied) glutamine synthetase (GS). GlnR-GS complex formation is also modulated by ATP and AMP. Thereby, gene repression exerted by the GlnR-GS complex is coupled with nitrogen (glutamine levels) and energetic status (ATP and AMP). Finally, we propose a DNA-looping model based on multiple operator sites that represents a strong and strict regulation for these genes.