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Structure paper

TitleppGpp regulates transcription elongation via direct and indirect inputs to RNA polymerase pausing and nucleotide addition.
Journal, issue, pagesBiorxiv, Year 2026
Publish dateMar 30, 2026 (structure data deposition date)
AuthorsAndreas U Mueller / Rachel A Mooney / Michael D Engstrom / Yu Bao / Michael B Wolfe / Balendra Sah / Jonathan Buscher / Jason Saba / James Liu / Seth A Darst / Robert Landick /
PubMed AbstractThe 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 ...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 , (p)ppGpp produced in response to charged-tRNA deficiency directly 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 allosterically stimulate RNAP pausing, inhibit catalysis, promote backtracking, compete for substrate GTP, inhibit GTP synthesis, or uncouple transcription-translation by inhibiting translation. Using a combination of cryo-EM, biochemical assays, and quantitative nascent elongating transcript sequencing (qNET-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 in vivo. (p)ppGpp stimulates swiveling at pause sites to delay escape but may also inhibit counter-swiveling required in every round of nucleotide addition.
External linksBiorxiv / PubMed:42182161 / PubMed Central
MethodsEM (single particle)
Resolution2.6 - 3.2 Å
Structure data

PDB-12eb:
Half-translocated RNA polymerase elemental paused elongation complex, swiveled with ppGpp (ePEC swiveled + ppGpp)
Method: ELECTRON MICROSCOPY / Resolution: 2.8 Å

PDB-12ec:
Half-translocated RNA polymerase elemental paused elongation complex, swiveled (ePEC swiveled)
Method: ELECTRON MICROSCOPY / Resolution: 2.6 Å

PDB-12ed:
Pre-translocated RNA polymerase elemental paused elongation complex, TL open with ppGpp (ePEC open + ppGpp)
Method: ELECTRON MICROSCOPY / Resolution: 3 Å

PDB-12ee:
Pre-translocated RNA polymerase elemental paused elongation complex, TL open (ePEC open)
Method: ELECTRON MICROSCOPY / Resolution: 2.8 Å

PDB-12ef:
Pre-translocated RNA polymerase elemental paused elongation complex, TL semiclosed with ppGpp (ePEC semiclosed + ppGpp)
Method: ELECTRON MICROSCOPY / Resolution: 3.1 Å

PDB-12eg:
Pre-translocated RNA polymerase elemental paused elongation complex, TL semiclosed (ePEC semiclosed)
Method: ELECTRON MICROSCOPY / Resolution: 2.8 Å

PDB-12eh:
Pre-translocated RNA polymerase elemental paused elongation complex, TL closed with ppGpp (ePEC closed + ppGpp)
Method: ELECTRON MICROSCOPY / Resolution: 3.2 Å

PDB-12ei:
Pre-translocated RNA polymerase elemental paused elongation complex, TL closed (ePEC closed)
Method: ELECTRON MICROSCOPY / Resolution: 2.8 Å

Chemicals

ChemComp-1N7:
CHAPSO / detergent*YM

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-G4P:
GUANOSINE-5',3'-TETRAPHOSPHATE

ChemComp-HOH:
WATER

Source
  • escherichia coli (E. coli)
KeywordsTRANSCRIPTION/DNA/RNA / elongation / pausing / pause escape / ppGpp / stringent response / TRANSCRIPTION / TRANSCRIPTION-DNA-RNA complex

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