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Research Themes DNA and RNA

Regulating nitrogen assimilation

SBKB [doi:10.1038/sbkb.2010.61]
Featured Article - January 2011
Short description: By combining their efforts, researchers at two PSI centers provide new insights into a switch that controls nitrogen metabolism in microorganisms.

Image courtesy of Wisedchaisri and Gonen.

Unlike animals, microorganisms and plants have the unique ability to reduce inorganic nitrogen to ammonium. However, this is an energetically costly process that must be tightly controlled to ensure long-term survivability. One way of regulating this process in some archaea and bacteria is through the protein NrpR, a 2-oxoglutarate (2OG)-sensitive homodimeric transcription factor.

In the absence of 2OG, NrpR binds DNA and represses the transcription of nitrogen assimilation genes. When 2OG is present, NrpR cannot bind DNA. A collaborative effort from researchers at two PSI centers (NYSGXRC and TEMIMPS) has now shed light on how 2OG binding affects NrpR structure and highlights the potential of combining the efforts of different centers.

As full-length NrpR was difficult to crystallize, Gonen and colleagues obtained crystals of the Methanocaldococcus jannaschii NrpR NRD2 domain dimers, revealing a highly conserved, deep cleft that bound 2OG in in silico docking experiments. Mutational analysis of Methanocaldococcus maripaludis NrpR confirmed this cleft as the 2OG-binding site, and 2OG prevented MmNrpR from binding target DNA. The authors were then able to use the crystal structure of MjNrpR-NRD2 to inform their analysis of the regulation of full-length MmNrpR by 2OG. Electron microscopy revealed that, in the absence of 2OG, dimeric NrpR exists in equilibrium between a square- or trapezium-shaped structure and a 'U'-shaped structure, with the latter being more prevalent. 2OG increases the abundance of the square-like structure, probably owing to reorientation of the three NrpR domains. In the U-shaped structure, the DNA-binding domains of the dimer are spaced properly for recognition of 'nitrogen operator' sequences; the 2OG-induced conformational changes increase the space between the domains and prevent sequence recognition. The exact mechanism by which 2OG induces these changes remains to be determined, but the combined efforts of these two PSI centers has provided a major step forward in the understanding of the regulation of nitrogen metabolism.

Steve Mason

References

  1. G. Wisedchaisri and D.M. Dranow et al. Structural underpinnings of nitrogen regulation by the prototypical nitrogen-responsive transcriptional factor NrpR.
    Structure 18, 1512-1521 (2010). doi:10.1016/j.str.2010.08.014

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