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PpGpp regulates transcription elongation via direct and indirect inputs to RNA polymerase

ABSTRACT: The signaling molecules guanosine 5′-tri/diphosphate 3′-diphosphate, (p)ppGpp, control bacterial protein synthesis rates and cell growth by targeting transcription, translation, NTP synthesis, and other functions. In lineages like E. coli, (p)ppGpp produced in response to charged-tRNA deficiency targets transcribing RNAP polymerase (RNAP) to match its pace to the pioneering ribosome on the nascent RNA (transcription–translation coupling). However, the mechanism by which (p)ppGpp slows RNAP is poorly defined. (p)ppGpp may stimulate RNAP pausing, inhibit catalysis, or promote backtracking allosterically, may inhibit GTP synthesis, may compete for GTP binding, or may uncouple transcription–translation by inhibiting ribosomes. Using a combination of cryo-EM, biochemical assays, quantitative nascent elongating transcript sequencing (qNET-seq), and quantitative ChIP-seq (qChIP-seq), we establish that (p)ppGpp allosterically regulates pausing and nucleotide addition via distinct motions of the RNAP swivel module and both competes with and lowers GTP. (p)ppGpp stimulates swiveling at pause sites to delay escape but may also inhibit counter-swiveling required in every round of nucleotide addition.

ORGANISM(S): Escherichia coli

PROVIDER: GSE327058 | GEO | 2026/08/07

REPOSITORIES: GEO

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