Amino acid starvation in Escherichia coli results in a spectrum of changes in gene expression, including inhibition of rRNA and tRNA promoters and activation of certain promoters for amino acid biosynthesis and transport. The unusual nucleotide ppGpp plays an important role in both negative and positive regulation. Previously, we and others suggested that positive effects of ppGpp might be indirect, resulting from the inhibition of rRNA transcription and, thus, liberation of RNA polymerase for binding to other promoters. Recently, we showed that DksA binds to RNA polymerase and greatly enhances direct effects of ppGpp on the negative control of rRNA promoters. This conclusion prompted us to reevaluate whether ppGpp might also have a direct role in positive control. We show here that ppGpp greatly increases the rate of transcription initiation from amino acid promoters in a purified system but only when DksA is present. Activation occurs by stimulation of the rate of an isomerization step on the pathway to open complex formation. Consistent with the model that ppGpp͞ DksA stimulates amino acid promoters both directly and indirectly in vivo, cells lacking dksA fail to activate transcription from the hisG promoter after amino acid starvation. Our results illustrate how transcription factors can positively regulate transcription initiation without binding DNA, demonstrate that dksA directly affects promoters in addition to those for rRNA, and suggest that some of the pleiotropic effects previously associated with dksA might be ascribable to direct effects of dksA on promoters involved in a wide variety of cellular functions.RNA polymerase ͉ rRNA transcription ͉ transcription initiation ͉ amino acid biosynthesis ͉ stringent response A mino acid starvation in Escherichia coli results in global changes in gene expression called the ''stringent response'' (reviewed in ref. 1). This regulatory response is initiated by entry of uncharged tRNAs into the A site of the ribosome and activation of the ribosome-associated RelA protein to synthesize the ''alarmone'' ppGpp (used here to refer to both guanosine 5Ј-diphosphate 3Ј-diphosphate and its pentaphosphate precursor). During starvation for amino acids, expression of stable RNA (rRNA and tRNA) is inhibited, whereas expression of enzymes for amino acid biosynthesis and transport is induced. These negative and positive responses are both relA dependent (e.g., refs. 2-6).ppGpp directly and specifically inhibits the initiation of transcription from stable RNA promoters in vivo and in vitro (7)(8)(9)(10)(11)(12). Although the details of the mechanism by which ppGpp exerts its effects on transcription initiation are still ill-defined, it has been shown that ppGpp decreases the lifetimes of competitorresistant complexes between RNA polymerase (RNAP) and all promoters that have been examined (12). The complex formed by RNAP at rRNA promoters is intrinsically short-lived, and ppGpp further decreases the lifetime of this complex. Thus, we have proposed that ppGpp shifts the equilibriu...