ppGpp Coordinates Nucleotide and Amino-Acid Synthesis in E. coli During Starvation

• Published in: Molecular cell Vol. 80; no. 1; pp. 29 - 42.e10
• Main Authors: Wang, Boyuan, Grant, Robert A., Laub, Michael T.
• Format: Journal Article
• Language: English
• Published: Elsevier Inc 01.10.2020
• Subjects: amino-acid synthesis; Gsk; ppGpp; pRpp; purine nucleotide synthesis; stringent response; ppGpp; purine nucleotide synthesis; amino-acid synthesis; pRpp; Gsk; stringent response
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2020.08.005

(p)ppGpp is a nucleotide messenger universally produced in bacteria following nutrient starvation. In E. coli, ppGpp inhibits purine nucleotide synthesis by targeting several different enzymes, but the physiological significance of their inhibition is unknown. Here, we report the structural basis of inhibition for one target, Gsk, the inosine-guanosine kinase. Gsk creates an unprecedented, allosteric binding pocket for ppGpp by restructuring terminal sequences, which restrains conformational dynamics necessary for catalysis. Guided by this structure, we generated a chromosomal mutation that abolishes Gsk regulation by ppGpp. This mutant strain accumulates abnormally high levels of purine nucleotides following amino-acid starvation, compromising cellular fitness. We demonstrate that this unrestricted increase in purine nucleotides is detrimental because it severely depletes pRpp and essential, pRpp-derived metabolites, including UTP, histidine, and tryptophan. Thus, our results reveal the significance of ppGpp’s regulation of purine nucleotide synthesis and a critical mechanism by which E. coli coordinates biosynthetic processes during starvation. [Display omitted] •E. coli inosine-guanosine kinase (Gsk) is a bona fide target of inhibition by ppGpp•ppGpp binds allosterically but in strong cooperation with the nucleoside substrate•Failure of ppGpp to inhibit Gsk/purine nucleotide synthesis causes ADP accumulation•High ADP inhibits pRpp-dependent synthesis of histidine and tryptophan, limiting growth Wang et al. demonstrate that ppGpp, the universally conserved growth regulator in bacteria, directly inhibits the purine nucleotide salvage enzyme Gsk. By characterizing a Gsk variant that is insensitive to ppGpp, they demonstrate that inhibiting purine nucleotide synthesis is required during starvation to maintain levels of the metabolite pRpp, which is required for synthesizing histidine and tryptophan.