Subsystem: Stringent Response, (p)ppGpp metabolism

This subsystem's description is:

Variant codes:

1 = organism contains a clear homolog of RelA or/and SpotT enzyme
-1 = no RelA or SpoT homologs can be asserted in a genome

The stringent response is a temporary inhibition of the synthesis of rRNA and tRNA when the cells are (i) starved for an amino acid, or (ii) are under carbon and energy limitation. It is mediated by signaling molecules guanosine tetraphosphate (ppGpp) and, to a lesser extend, guanosine pentaphosphate (pppGpp), which together are referred to as (p)ppGpp.
Synthesis of (p)ppGpp in E. coli occurs in two ways. One route is mediated by RelA, a (p)ppGpp synthetase I - ribosome associated protein, which catalyzes the transfer of a pyrophosphoryl group from ATP to either GTP or GDP, producing pppGpp or ppGpp in response to ribosome “idling”. This happens when a ribosome is stalled due to insufficient supply of aminoacylated tRNA, caused by the starvation for amino acid(s). In E. coli the pppGpp, generated by RelA, is subsequently degraded to ppGpp by Guanosine-5'-triphosphate,3'-diphosphate pyrophosphatase, encoded by the gpp gene.

The cellular level of (p)ppGpp is influenced also by its degradation, catalyzed by guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase SpoT

The second, RelA independent pathway of (p)ppGpp biosynthesis is mediated by SpoT protein. SpoT is believed to be a bifunctional enzyme, that both, synthesizes and degrades (p)ppGpp. The ratio of biosynthesis and degradation is somehow regulated by carbon and energy limitation (reviewed in refs. 1, 2)

Situation in Archaea is very different. According to (Cellini et al., 2004): (p)ppGpp appears to be completely absent from the Archaea and thus constitutes an additional feature that distinguishes the Bacteria from the Archaea. However, (1) stringency is widespread in wild-type thermoacidophilic archaea; (2) in the crenarchaeal species stringent control (SC) depends on the deaminoacylation of tRNA; (3) in the strains analyzed ppGpp is not produced during normal growth nor during the stringent reaction; it is therefore not an effector either of SC over sRNA synthesis or of growth control (Cellini et al., 2004)

Several AUXILIARY Functional Roles were included in this Subsystem based merely on the conserved co-localization of the corresponding genes with relA or spoT. Notably, phosphoribosyltransferase, which catalyzes reversible transfer of the phosphoribosyl group from 5-phospho--D-ribosyl 1-pyrophosphate (PRPP) to adenine (or guanine, or hypoxanthine) is located in the vicinity of relA homologs (and spoT - to a lesser extend) in many diverse genomes.

For more information, please check out the description and the additional notes tabs, below

DiagramFunctional RolesSubsystem SpreadsheetDescriptionAdditional NotesScenarios 

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Group Alias
Abbrev.Functional RoleReactionsScenario ReactionsGOLiterature

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