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SpoT is a bacterial protein that hydrolizes alarmones, (p)ppGpp, in the bacterial stringent response. Its hydrolase activity is Mn2+-dependent with a conserved His-Asp (HD) motif. In E. coli, SpoT protein consists of 693 amino acids. SpoT belongs to the RSH protein family. It is bifunctional, has both hydrolase and synthase activities. When relA is deleted, E. coli still can produce (p)ppGpp by SpoT.

SpoT can sense many sources of nutrient stress other than amino acid starvation and to respond by limiting hydrolase. The acyl carrier protein (ACP) binds to the TGS domain of SpoT; this binding is probably influenced by the ratio of unacylated ACP to acylated ACP in the cell. Fatty acid starvation leads to a shift in the balance of the two SpoT activities in favor of synthesis. Phosphate starvation is sensed by SpoT hydrolase to elevate (p)ppGpp, which induces IraP, a RssB antiadaptor that antagonizes RssB activation of RpoS turnover, thereby inducing RpoS.