Control of spoT-dependent ppGpp synthesis and degradation in Escherichia coli

J Mol Biol. 1996 May 31;259(1):41-57. doi: 10.1006/jmbi.1996.0300.


Escherichia coli has two ppGpp synthetases, PSI and PSII, encoded by the relA and spoT genes. The spoT gene also encodes a ppGpp hydrolase. During exponential growth and under various starvation conditions, the level of ppGpp depends on the balance of ppGpp synthetic and degradative activities of spoT gene products. To find out how these two activities respond to different physiological conditions and to learn about the signals involved in these responses, rates of ppGpp synthesis and degradation were determined in an E. coli B/r delta relA strain during: (1) multiple amino acid deprivation after a nutritional shift-down from glucose amino acids to glucose minimal medium; (2) carbon source starvation after a "glucose runout"; (3) energy starvation by treatment with sodium azide. To each of these conditions, bacteria responded with a similar gradual accumulation of ppGpp, occurring over a period of 20 to 40 minutes, from the basal level of 4 and 24 pmol/OD460 in glucose amino acids and glucose minimal medium, respectively, to about 100 pmol ppGpp/OD460 unit of culture mass. After multiple amino acid deprivation and during azide treatment, the rate of ppGpp synthesis increased and the rate of ppGpp degradation decreased, but in different proportions by the two kinds of treatment. After glucose runout, both ppGpp synthesis and degradation immediately decreased, but the rate of degradation was reduced more, which caused the accumulation of ppGpp despite its reduced synthesis. ppGpp synthesis required continuous protein synthesis, but ppGpp hydrolysis and its control did not: the rate of ppGpp degradation could be instantly up or down-regulated in response to changes in exogenous amino acid or glucose levels in the absence of protein synthesis. The results suggest that PSII is unstable with an average functional lifetime of 40 seconds or less, and that its activity is generated during or shortly after spoT mRNA translation in response to the availability of amino acids. This regulation is responsible for the growth medium-dependent changes in basal levels of ppGpp. ppGpp hydrolysis is controlled, i.e. inhibited, mainly during conditions of physiological stress, such as multiple amino acid deprivation or energy deprivation. This inhibition can be correlated with an inferred accumulation of uncharged tRNA. Since previous reports have indicated that uncharged tRNA inhibits purified SpoT hydrolase in vitro, it is proposed that ppGpp hydrolase activity is, indeed, controlled by the concentration of uncharged tRNA in the cell. Finally, it was found that neither relC, transcriptional regulation of spoT, nor different translation starts of spoT mRNA are directly involved in the environmental control of SpoT hydrolase and PSII activities.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acids / metabolism
  • Azides / metabolism
  • Azides / pharmacology
  • Culture Media
  • Escherichia coli / genetics
  • Escherichia coli / growth & development
  • Escherichia coli / metabolism*
  • Glucose / metabolism
  • Glucose / pharmacology
  • Guanosine Tetraphosphate / biosynthesis
  • Guanosine Tetraphosphate / metabolism*
  • Hydrolysis
  • Mutagens / metabolism
  • Mutagens / pharmacology
  • Protein Biosynthesis
  • Pyrophosphatases / genetics
  • Pyrophosphatases / metabolism*
  • RNA, Messenger / metabolism
  • RNA, Transfer / metabolism
  • Sodium Azide


  • Amino Acids
  • Azides
  • Culture Media
  • Mutagens
  • RNA, Messenger
  • Guanosine Tetraphosphate
  • RNA, Transfer
  • Sodium Azide
  • guanosine-3',5'-bis(diphosphate) 3'-pyrophosphatase
  • Pyrophosphatases
  • Glucose