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Ammonia is a major signal that regulates nitrogen fixation in most diazotrophs. Regulation of nitrogen fixation by ammonia in the Gram-negative diazotrophs is well-characterized. In these bacteria, this regulation occurs mainly at the level of  nif  ( ni trogen  f ixation) gene transcription, which requires a  nif -specific activator, NifA. Although Gram-positive and diazotrophic  Paenibacilli  have been extensively used as a bacterial fertilizer in agriculture, how nitrogen fixation is regulated in response to nitrogen availability in these bacteria remains unclear. An indigenous GlnR and GlnR/TnrA-binding sites in the promoter region of the  nif  cluster are conserved in these strains, indicating the role of GlnR as a regulator of nitrogen fixation. In this study, we for the first time reveal that GlnR of  Paenibacillus polymyxa  WLY78 is essentially required for  nif  gene transcription under nitrogen limitation, whereas both GlnR and glutamine synthetase (GS) encoded by  glnA  within  glnRA  operon are required for repressing  nif  expression under excess nitrogen. Dimerization of GlnR is necessary for binding of GlnR to DNA. GlnR in  P .  polymyxa  WLY78 exists in a mixture of dimers and monomers. The C-terminal region of GlnR monomer is an autoinhibitory domain that prevents GlnR from binding DNA. Two GlnR-biding sites flank the -35/-10 regions of the  nif  promoter of the  nif  operon ( nifBHDKENXhesAnifV ). The GlnR-binding site Ⅰ (located upstream of -35/-10 regions of the  nif  promoter) is specially required for activating  nif  transcription, while GlnR-binding siteⅡ (located downstream of -35/-10 regions of the  nif  promoter) is for repressing  nif  expression. Under nitrogen limitation, GlnR dimer binds to GlnR-binding siteⅠ in a weak and transient association way and then activates  nif  transcription. During excess nitrogen, glutamine binds to and feedback inhibits GS by forming the complex FBI-GS. The FBI-GS interacts with the C-terminal domain of GlnR and stabilizes the binding affinity of GlnR to GlnR-binding site Ⅱ and thus represses  nif  transcription.

Positive and negative regulation of transferred nif genes mediated by indigenous GlnR in Gram-positive Paenibacillus polymyxa