Molecular mechanism and evolution of guanylate kinase regulation by (p)ppGpp

Mol Cell. 2015 Feb 19;57(4):735-749. doi: 10.1016/j.molcel.2014.12.037. Epub 2015 Feb 5.


The nucleotide (p)ppGpp mediates bacterial stress responses, but its targets and underlying mechanisms of action vary among bacterial species and remain incompletely understood. Here, we characterize the molecular interaction between (p)ppGpp and guanylate kinase (GMK), revealing the importance of this interaction in adaptation to starvation. Combining structural and kinetic analyses, we show that (p)ppGpp binds the GMK active site and competitively inhibits the enzyme. The (p)ppGpp-GMK interaction prevents the conversion of GMP to GDP, resulting in GMP accumulation upon amino acid downshift. Abolishing this interaction leads to excess (p)ppGpp and defective adaptation to amino acid starvation. A survey of GMKs from phylogenetically diverse bacteria shows that the (p)ppGpp-GMK interaction is conserved in members of Firmicutes, Actinobacteria, and Deinococcus-Thermus, but not in Proteobacteria, where (p)ppGpp regulates RNA polymerase (RNAP). We propose that GMK is an ancestral (p)ppGpp target and RNAP evolved more recently as a direct target in Proteobacteria.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacteria / enzymology*
  • Bacteria / genetics
  • Bacteria / metabolism
  • Bacterial Proteins / metabolism*
  • Binding, Competitive
  • Catalytic Domain
  • Crystallography, X-Ray
  • DNA-Directed RNA Polymerases / metabolism
  • Evolution, Molecular*
  • Guanosine Pentaphosphate / chemistry
  • Guanosine Pentaphosphate / metabolism*
  • Guanosine Tetraphosphate / chemistry
  • Guanosine Tetraphosphate / metabolism*
  • Guanosine Triphosphate / metabolism
  • Guanylate Kinases / chemistry
  • Guanylate Kinases / metabolism*
  • Models, Biological
  • Species Specificity
  • Stress, Physiological


  • Bacterial Proteins
  • Guanosine Tetraphosphate
  • Guanosine Pentaphosphate
  • Guanosine Triphosphate
  • Guanylate Kinases
  • DNA-Directed RNA Polymerases

Associated data

  • PDB/4QRH