title: Molecular mechanism and evolution of guanylate kinase regulation by (p)ppGpp.
abstract: 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.
authors: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
authors: Kuanqing
authors: K
authors: Liu
authors: Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors: Angela R
authors: AR
authors: Myers
authors: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors: Tippapha
authors: T
authors: Pisithkul
authors: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors: Kathy R
authors: KR
authors: Claas
authors: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biophysics, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors: Kenneth A
authors: KA
authors: Satyshur
authors: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors: Daniel
authors: D
authors: Amador-Noguez
authors: Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors: James L
authors: JL
authors: Keck
authors: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA. Electronic address: wang@bact.wisc.edu.
authors: Jue D
authors: JD
authors: Wang
mesh_terms: D001419:Bacteria / Q000201:enzymology* / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000378:metabolism*; D001667:Binding, Competitive; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D019143:Evolution, Molecular; D006158:Guanosine Pentaphosphate / Q000737:chemistry / Q000378:metabolism*; D006159:Guanosine Tetraphosphate / Q000737:chemistry / Q000378:metabolism*; D006160:Guanosine Triphosphate / Q000378:metabolism; D051528:Guanylate Kinases / Q000737:chemistry / Q000378:metabolism*; D008954:Models, Biological; D013045:Species Specificity; D013312:Stress, Physiological
chemical_list: D001426:Bacterial Proteins; D006159:Guanosine Tetraphosphate; D006158:Guanosine Pentaphosphate; D006160:Guanosine Triphosphate; D051528:Guanylate Kinases; D012321:DNA-Directed RNA Polymerases